pc_compinfo: Retrieve compound information from pubchem CID

Description

Retrieve compound information from pubchem CID, see https://pubchem.ncbi.nlm.nih.gov/

Usage

pc_compinfo(cid, first = FALSE, verbose = TRUE, ...)

Arguments

cid

character; Pubchem ID (CID).

first

logical; return only first list items? That is: a list with entries of lenght 1 (for easy conversion in a data.frame)

verbose

logical; should a verbose output be printed on the console?

...

currently not used.

Value

a list with entries: CID (Pubchem ID), InChIKey, InChI, synonyms, IUPACName, Canonical SMILES, Isomeric SMILES, MolecularFormula, MolecularWeight, TotalFormalCharge, XlogP, HydrogenBondDonorCount, HydrogenBondAcceptorCount, Complexity, HeavyAtomCount, AtomChiralCount, AtomChiralDefCount, AtomChiralUndefCount, BondChiralCount, BondChiralDefCount, BondChiralUndefCount, IsotopeAtomCount, CovalentUnitCount, TautomerCount and source_url

References

Wang, Y., J. Xiao, T. O. Suzek, et al. 2009 PubChem: A Public Information System for Analyzing Bioactivities of Small Molecules. Nucleic Acids Research 37: 623–633.

Kim, Sunghwan, Paul A. Thiessen, Evan E. Bolton, et al. 2016 PubChem Substance and Compound Databases. Nucleic Acids Research 44(D1): D1202–D1213.

Examples

Run this code

# might fail if API is not available
cid <- get_pcid('Triclosan')
pc_compinfo(cid[1])

###
# multiple CIDS
comp <- c('Triclosan', 'Aspirin')
cids <- sapply(comp, function(x) get_pcid(x, first = TRUE))
(ll <- lapply(cids, pc_compinfo, first = TRUE))
# as mtrix
do.call(rbind, ll)