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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-27 16:11:25 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-27 16:11:25 +0200
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+
+ <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 &#39;source&#39;</dd></p>
+
+ <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute &#39;source&#39;</dd></p>
+
+ <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute &#39;source&#39;</dd></p>
+
+ <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute &#39;source&#39;</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">&lt;-</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'>&lt;chent&gt;
+Identifier $identifier 1-octanol
+InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N
+SMILES string $smiles:
+ user PubChem_Canonical
+ &quot;CCCCCCCCO&quot; &quot;CCCCCCCCO&quot;
+Molecular weight $mw: 130.2
+PubChem synonyms (up to 10):
+ [1] &quot;957&quot; &quot;1-octanol&quot; &quot;Octan-1-ol&quot; &quot;octanol&quot;
+ [5] &quot;N-octanol&quot; &quot;Octyl alcohol&quot; &quot;Capryl alcohol&quot; &quot;n-Octyl alcohol&quot;
+ [9] &quot;caprylic alcohol&quot; &quot;111-87-5&quot;
+</div>
+<div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">oct</span><span class="keyword">)</span></div>
+<div class='input'><span class="symbol">caffeine</span> <span class="assignement">&lt;-</span> <span class="symbol">chent</span><span class="keyword">$</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'>&lt;chent&gt;
+Identifier $identifier caffeine
+InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N
+SMILES string $smiles:
+ PubChem_Canonical
+&quot;CN1C=NC2=C1C(=O)N(C(=O)N2C)C&quot;
+Molecular weight $mw: 194.2
+PubChem synonyms (up to 10):
+ [1] &quot;2519&quot; &quot;caffeine&quot;
+ [3] &quot;1,3,7-Trimethylxanthine&quot; &quot;Methyltheobromine&quot;
+ [5] &quot;Guaranine&quot; &quot;Cafeina&quot;
+ [7] &quot;Koffein&quot; &quot;Mateina&quot;
+ [9] &quot;Thein&quot; &quot;Theine&quot;
+</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>
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