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diff --git a/docs/chent.html b/docs/chent.html new file mode 100644 index 0000000..0f4a43d --- /dev/null +++ b/docs/chent.html @@ -0,0 +1,180 @@ +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<title>chent. 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 chemical entities with associated data</h1> + +<div class="row"> + <div class="span8"> + <h2>Usage</h2> + <pre><span class="symbol">chent</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. Chemical information is retrieved from +the internet. Additionally, it can be generated using RDKit if RDKit and its +python bindings are installed and configured for use with PythonInR.</p> + + </div> + + <div class="Fields"> + <h2>Fields</h2> + + <p></p> + + <p><dl> +<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute 'source'</dd></p> + + <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute 'source'</dd></p> + + <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute 'source'</dd></p> + + <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute 'source'</dd></p> + + <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p> + + <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit, if installed and +configured for use with PythonInR</dd></p> + + <p><dt><code>Picture</code></dt><dd>Graph as a <code><a href='http://www.rdocumentation.org/packages/grImport/topics/picture'>picture</a></code> object obtained using grImport</dd></p> + + <p><dt><code>chyaml</code></dt><dd>List of information obtained from a YAML file</dd></p> + + <p><dt><code>degradation</code></dt><dd>List of degradation endpoints</dd></p> + + <p></dl></p> + + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class="symbol">oct</span> <span class="assignement"><-</span> <span class="symbol">chent</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">"1-octanol"</span><span class="keyword">,</span> <span class="argument">smiles</span> <span class="argument">=</span> <span class="string">"CCCCCCCCO"</span><span class="keyword">)</span></div> +<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'>Loading required namespace: PythonInR</strong> +<strong class='message'> +Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) +[GCC 4.9.2] +</strong> +<strong class='message'>Trying to get chemical information from RDKit using user SMILES +CCCCCCCCO</strong> +<strong class='message'>Did not find chyaml file ./1-octanol.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">oct</span><span class="keyword">)</span></div> +<div class='output'><chent> +Identifier $identifier 1-octanol +InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N +SMILES string $smiles: + user PubChem_Canonical + "CCCCCCCCO" "CCCCCCCCO" +Molecular weight $mw: 130.2 +PubChem synonyms (up to 10): + [1] "957" "1-octanol" "Octan-1-ol" "octanol" + [5] "N-octanol" "Octyl alcohol" "Capryl alcohol" "n-Octyl alcohol" + [9] "caprylic alcohol" "111-87-5" +</div> +<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">oct</span><span class="keyword">)</span></div> +<div class='input'><span class="symbol">caffeine</span> <span class="assignement"><-</span> <span class="symbol">chent</span><span class="keyword">$</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/methods/topics/new'>new</a></span><span class="keyword">(</span><span class="string">"caffeine"</span><span class="keyword">)</span></div> +<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 +CN1C=NC2=C1C(=O)N(C(=O)N2C)C</strong> +<strong class='message'>Did not find chyaml file ./caffeine.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">caffeine</span><span class="keyword">)</span></div> +<div class='output'><chent> +Identifier $identifier caffeine +InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N +SMILES string $smiles: + PubChem_Canonical +"CN1C=NC2=C1C(=O)N(C(=O)N2C)C" +Molecular weight $mw: 194.2 +PubChem synonyms (up to 10): + [1] "2519" "caffeine" + [3] "1,3,7-Trimethylxanthine" "Methyltheobromine" + [5] "Guaranine" "Cafeina" + [7] "Koffein" "Mateina" + [9] "Thein" "Theine" +</div> +<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">caffeine</span><span class="keyword">)</span></div> +<p><img src='chent-25.png' alt='' width='540' height='400' /></p></pre> + </div> + <div class="span4 sidebar"> + <!-- <ul> + <li>chent</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 href="https://github.com/hadley/staticdocs">staticdocs</a>. 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