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authorJohannes Ranke <jranke@uni-bremen.de>2021-11-19 00:22:03 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-11-19 00:22:03 +0100
commit79123acfdd9a9b905a5b177e2b7aa0d604e52267 (patch)
tree010dbecd40bddb46aafb0bc6c8da8a1ced08532a /docs/reference/pai.html
parent0056584e5168df75bca159ddf3469aa07457b77d (diff)
Add plot example, update static docs
Diffstat (limited to 'docs/reference/pai.html')
-rw-r--r--docs/reference/pai.html155
1 files changed, 113 insertions, 42 deletions
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index e240e11..e5ecb99 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -8,21 +8,29 @@
<title>An R6 class for pesticidal active ingredients and associated data — pai • chents</title>
+
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-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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@@ -30,11 +38,11 @@
-<meta property="og:title" content="An R6 class for pesticidal active ingredients and associated data — pai" />
+<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" />
+
@@ -48,9 +56,10 @@ Additional chemical information is retrieved from the internet if available." />
<![endif]-->
+
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+ <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -64,7 +73,7 @@ Additional chemical information is retrieved from the internet if available." />
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<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 class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.3.1</span>
</span>
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@@ -72,7 +81,7 @@ Additional chemical information is retrieved from the internet if available." />
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+ <span class="fas fa-home fa-lg"></span>
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@@ -80,11 +89,10 @@ Additional chemical information is retrieved from the internet if available." />
<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 href="https://github.com/jranke/chents/">
+ <span class="fab fa-github fa-lg"></span>
</a>
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@@ -95,6 +103,7 @@ Additional chemical information is retrieved from the internet if available." />
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+
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<div class="row">
@@ -106,30 +115,92 @@ Additional chemical information is retrieved from the internet if available." />
</div>
<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>
<p>An <code>R6Class</code> generator object</p>
-
- <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
+ <h2 class="hasAnchor" id="super-class"><a class="anchor" href="#super-class"></a>Super class</h2>
+
+ <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>
+
+<dt><code>bcpc</code></dt><dd><p>List of information retrieved from pesticidecompendium.bcpc.org</p></dd>
+
+</dl><p></div></p>
+ <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2>
- <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>
-
+<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'>$</span><span class='fu'>clone</span><span class='op'>(</span>deep <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre><p></div></p>
+
+<h4 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Arguments</h4>
+<p><div class="arguments"></p><dl>
+<dt><code>deep</code></dt><dd><p>Whether to make a deep clone.</p></dd>
+
+</dl><p></div></p>
+
+
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>atr</span> <span class='kw'>&lt;-</span> <span class='no'>pai</span>$<span class='fu'>new</span>(<span class='st'>"atrazine"</span>)</div><div class='output co'>#&gt; <span class='message'>alanwood.net:</span></div><div class='output co'>#&gt; <span class='message'>Querying atrazine.html</span></div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/inchikey/cids/JSON</span></div><div class='output co'>#&gt; <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'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</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='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'>#&gt; &lt;pai&gt; with ISO common name $iso atrazine
+ <pre class="examples"><div class='input'><span class='va'>atr</span> <span class='op'>&lt;-</span> <span class='va'>pai</span><span class='op'>$</span><span class='fu'>new</span><span class='op'>(</span><span class='st'>"atrazine"</span><span class='op'>)</span>
+</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='input'><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>
+</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
@@ -138,36 +209,36 @@ Additional chemical information is retrieved from the internet if available.</p>
#&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C"
#&gt; Molecular weight $mw: 215.7
#&gt; PubChem synonyms (up to 10):
-#&gt; [1] "2256" "atrazine" "1912-24-9" "Gesaprim" "Chromozin"
-#&gt; [6] "Oleogesaprim" "Aktikon" "Argezin" "Atazinax" "Atranex" </div></pre>
+#&gt; [1] "atrazine" "1912-24-9" "Gesaprim" "Oleogesaprim" "Chromozin"
+#&gt; [6] "Aktikon" "Atrazin" "Argezin" "Atazinax" "Atranex" </div><div class='input'><span class='kw'>if</span> <span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NULL.html'>is.null</a></span><span class='op'>(</span><span class='va'>atr</span><span class='op'>$</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>
+</div><div class='img'><img src='pai-1.png' alt='' width='700' height='433' /></div></pre>
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- <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>
-
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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