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diff --git a/docs/reference/chent.html b/docs/reference/chent.html new file mode 100644 index 0000000..15c4d10 --- /dev/null +++ b/docs/reference/chent.html @@ -0,0 +1,160 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>An R6 class for chemical entities with associated data — chent • chents</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">chents</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>An R6 class for chemical entities with associated data</h1> + </div> + + + <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> + + + <pre><span class='no'>chent</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> + + <p></p> + <p><dl class='dl-horizontal'> +<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>svg</code></dt><dd>SVG code</dd></p> + <p><dt><code>Picture</code></dt><dd>Graph as a <code>picture</code> object obtained using grImport</dd></p> + <p><dt><code>Pict_font_size</code></dt><dd>Font size as extracted from the intermediate PostScript file</dd></p> + <p><dt><code>pdf_height</code></dt><dd>Height of the MediaBox in the pdf after cropping</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> +</dl></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</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/name/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'></span> +#> <span class='message'>Initialize Python Version 3.4.2 (default, Oct 8 2014, 10:47:48) </span> +#> <span class='message'>[GCC 4.9.1]</span></div><div class='output co'>#> <span class='message'>Trying to get chemical information from RDKit using user SMILES</span> +#> <span class='message'>CCCCCCCCO</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#> <chent> +#> Identifier $identifier 1-octanol +#> InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N +#> SMILES string $smiles: +#> user PubChem_Canonical +#> "CCCCCCCCO" "CCCCCCCCO" +#> Molecular weight $mw: 130.2 +#> PubChem synonyms (up to 10): +#> [1] "957" "1-octanol" "Octan-1-ol" "octanol" +#> [5] "Octyl alcohol" "N-octanol" "Capryl alcohol" "n-Octyl alcohol" +#> [9] "111-87-5" "caprylic alcohol"</div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'><-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</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/name/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'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#> <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>caffeine</span>)</div><div class='output co'>#> <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] "Guaranine" "1,3,7-Trimethylxanthine" +#> [5] "Methyltheobromine" "Cafeina" +#> [7] "Thein" "Koffein" +#> [9] "Mateina" "Theine" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='chent-22.png' alt='' width='540' height='400' /></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> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + 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