chents 0.2-3

An R6 class for chemical entities with associated data

Usage

chent

Format

An R6Class generator object

Description

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.

Fields

identifier
The identifier that was used to initiate the object, with attribute 'source'

inchikey
InChI Key, with attribute 'source'

smiles
SMILES code, with attribute 'source'

mw
Molecular weight, with attribute 'source'

pubchem
List of information retreived from PubChem

rdkit
List of information obtained with RDKit, if installed and configured for use with PythonInR

Picture
Graph as a picture object obtained using grImport

chyaml
List of information obtained from a YAML file

degradation
List of degradation endpoints

Examples

oct <- chent$new("1-octanol", smiles = "CCCCCCCCO")

PubChem:
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
Found 1 entries in PubChem, using the first one.
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
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
Loading required namespace: PythonInR

Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) 
[GCC 4.9.2]

Trying to get chemical information from RDKit using user SMILES
CCCCCCCCO
Did not find chyaml file ./1-octanol.yaml

print(oct)


<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"        



plot(oct)


caffeine <- chent$new("caffeine")

PubChem:
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON
Found 1 entries in PubChem, using the first one.
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
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON
Trying to get chemical information from RDKit using PubChem_Canonical SMILES
CN1C=NC2=C1C(=O)N(C(=O)N2C)C
Did not find chyaml file ./caffeine.yaml

print(caffeine)


<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"                 



plot(caffeine)