Get PubChem Substance Information

Description

The PubChem substance collection stores a variety of information for each molecule. These include canonical SMILES, molecular properties, substance associations, synonyms etc.

This function will extract a subset of the molecular property information for one or more compound ID's

Usage

1
get.sid(sid, quiet=TRUE, from.file=FALSE)

Arguments

sid

A vector of one or more compound ID's

quiet

If FALSE, output is verbose

from.file

If TRUE then the first argument is considered to be the name of a file containing the XML data. If FALSE the first argument must be a sequence of compound ID's and the data will be downloaded from the PubChem FTP site

Details

Processing a large number of substance ID's can take a long time. For large numbers of SID's the resultant XML file can be many megabytes. This may take a long time to download. After download it takes approximate 20 sec to process a 23MB data file.

It should also be noted that the data files are downloaded using the R interface to Curl. In addition, the PubChem servers do not allow very large query URL's. This limits the number of substance ID's that can be directly pulled of the PubChem servers to about 1000

Value

A data.frame with 9 columns:

SID

The substance ID

IUPACName

The IUPAC name of the compound

CanonicalSmiles

The canonical SMILES for the compound

MolecularWeight

Molecular weight

TotalFormalCharge

The formal charge

MolecularFormula

The molecular formula

TPSA

Topological polar surface area

HeavyAtomCount

Heavy atom count

FormalCharge

Total formal charge

HydrogenBondDonor

Hydrogen bond donor count

HydrogenBondAcceptor

Hydrogen bond acceptor count

Author(s)

Rajarshi Guha rajarshi.guha@gmail.com

See Also

get.assay, get.cid, get.sid.list