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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 '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>
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