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diff --git a/docs/pai.html b/docs/pai.html new file mode 100644 index 0000000..61b1722 --- /dev/null +++ b/docs/pai.html @@ -0,0 +1,134 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>pai. chents 0.2-3</title> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="author" content=""> + +<link href="css/bootstrap.css" rel="stylesheet"> +<link href="css/bootstrap-responsive.css" rel="stylesheet"> +<link href="css/highlight.css" rel="stylesheet"> +<link href="css/staticdocs.css" rel="stylesheet"> + +<!--[if lt IE 9]> + <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<![endif]--> + +<script type="text/x-mathjax-config"> + MathJax.Hub.Config({ + tex2jax: { + inlineMath: [ ['$','$'], ["\\(","\\)"] ], + processEscapes: true + } + }); +</script> +<script type="text/javascript" + src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> +</script> + </head> + + <body> + <div class="navbar"> + <div class="navbar-inner"> + <div class="container"> + <a class="brand" href="index.html">chents 0.2-3</a> + <div class="nav"> + <ul class="nav"> + <li><a href="index.html">Home</a></li> + <li><a href="reference.html">Reference</a></li> + </ul> + </div> + </div> + </div> +</div> + + + <div class="container"> + <header> + + </header> + + <h1>An R6 class for pesticidal active ingredients and associated data</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="symbol">pai</span></pre> + + <div class="Format"> + <h2>Format</h2> + + <p>An <code><a href='http://www.rdocumentation.org/packages/R6/topics/R6Class'>R6Class</a></code> generator object</p> + + </div> + + <div class="Description"> + <h2>Description</h2> + + <p>The class is initialised with an identifier which is generally an ISO common name. +Additional chemical information is retrieved from the internet.</p> + + </div> + + <div class="Fields"> + <h2>Fields</h2> + + <p></p> + + <p><dl> +<dt><code>iso</code></dt><dd>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</dd></p> + + <p><dt><code>alanwood</code></dt><dd>List of information retreived from www.alanwood.net/pesticides</dd></p> + + <p></dl></p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class="symbol">atr</span> <span class="assignement"><-</span> <span class="symbol">pai</span><span class="keyword">$</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/methods/topics/new'>new</a></span><span class="keyword">(</span><span class="string">"atrazine"</span><span class="keyword">)</span></div> +<strong class='message'>alanwood.net:</strong> +<strong class='message'>Querying atrazine.html</strong> +<strong class='message'>PubChem:</strong> +<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</strong> +<strong class='message'>Found 1 entries in PubChem, using the first one.</strong> +<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,ExactMass,MonoisotopicMass,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount,RotatableBondCount,HeavyAtomCount,IsotopeAtomCount,AtomStereoCount,DefinedAtomStereoCount,UndefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,UndefinedBondStereoCount,CovalentUnitCount,Volume3D,XStericQuadrupole3D,YStericQuadrupole3D,ZStericQuadrupole3D,FeatureCount3D,FeatureAcceptorCount3D,FeatureDonorCount3D,FeatureAnionCount3D,FeatureCationCount3D,FeatureRingCount3D,FeatureHydrophobeCount3D,ConformerModelRMSD3D,EffectiveRotorCount3D,ConformerCount3D,Fingerprint2D/JSON</strong> +<strong class='message'>http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</strong> +<strong class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES +CCNC1=NC(=NC(=N1)Cl)NC(C)C</strong> +<strong class='message'>Did not find chyaml file ./atrazine.yaml</strong> +<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">atr</span><span class="keyword">)</span></div> +<div class='output'><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" "Fenatrol" "Atranex" "Atred" + [7] "Atazinax" "Atrasine" "Chromozin" "Gesaprim" +</div></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>pai</li> + </ul> + <ul> + <li>data</li> + </ul> --> + + + + + </div> +</div> + + <footer> + <p class="pull-right"><a href="#">Back to top</a></p> +<p>Built by <a 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