chents 0.2-1

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.

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

Picture
Graph as a picture object obtained using grImport

Examples

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


http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&db=pccompound&term=1-octanol
Found 1 entries in PubChem, using the first one.
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&db=pccompound&ID=957

print(oct)



<chent>
Identifier $identifier 1-octanol 
InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
SMILES string $smiles CCCCCCCCO 
Molecular weight $mw: 130.2 
PubChem synonyms (first 10):
 [1] "1-octanol"        "Octan-1-ol"       "octanol"          "N-octanol"        "Capryl alcohol"   "Octyl alcohol"   
 [7] "n-Octyl alcohol"  "caprylic alcohol" "Heptyl carbinol"  "1-Hydroxyoctane" 



plot(oct)



caffeine <- chent$new("caffeine", source = "pubchem")


http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?retmax=100000&db=pccompound&term=caffeine
Found 217 entries in PubChem, using the first one.
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?retmax=100000&db=pccompound&ID=1188

print(caffeine)



<chent>
Identifier $identifier caffeine 
InChI Key $inchikey LRFVTYWOQMYALW-UHFFFAOYSA-N 
SMILES string $smiles C1=NC2=C(N1)C(=O)NC(=O)N2 
Molecular weight $mw: 152.1 
PubChem synonyms (first 10):
 [1] "xanthine"            "2,6-Dihydroxypurine" "69-89-6"             "Xanthin"             "2,6-dioxopurine"    
 [6] "Pseudoxanthine"      "Isoxanthine"         "Xanthic oxide"       "1H-Purine-2,6-diol"  "Purine-2,6-diol"    



caffeine$get_rdkit()
plot(caffeine)