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diff --git a/docs/chent.html b/docs/chent.html deleted file mode 100644 index 0f4a43d..0000000 --- a/docs/chent.html +++ /dev/null @@ -1,180 +0,0 @@ -<!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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