getcid: Get PubChem Compound Information

In rpubchem: An Interface to the PubChem Collection

Description

The PubChem compound 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 a single CID.

Usage

get.cid(cid, quiet=TRUE)

Arguments

cid	A single numeric CID
quiet	If FALSE, output is verbose

Details

The method currently queries PubChem via the PUG REST interface. Since the method processes a single CID at a time, the user can parallelize processing. However, this is usually not recommended, at least in an unrestricted manner.

In addition, since the data.frame for each CID may have a different set of physical properties, it is recommended to either extract the common set of columns or else use something like bind_rows from the dplyr package to get a uniform data.frame if processing multiple CIDs

Value

A data.frame with at least 23 columns including the CID, IUPAC name, InChI and InChI key, canonical SMILES and a variety of molecular descriptors. In addition, a few physical properties are also included.

Author(s)

Rajarshi Guha [e-mail]

See Also

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

Examples

## Not run: 
cids <- c(5282108, 5282148, 91754124)
dat <- lapply(cids, get.cid)
dat <- dplyr::bind_rows(dat)
str(dat)

## End(Not run)

rpubchem documentation built on May 2, 2019, 4:33 a.m.