getPCID.smiles: Retrieve PubChem CIDs from SMILES or InChI

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

Retrieves PubChem CIDs from SMILES or InChI using PUG REST. By "default", this also returns the CID of the prefered tautomer according to current PubChem standardization procedures

Usage

getPCID.smiles(query, from = "smiles", to="cids", timeout=30)

Arguments

query	SMILES or InChI (or other) to be converted
from	Type of input ID (default "smiles", i.e. SMILES, alternative "inchi" to retrieve via InChI, or others (untried))
timeout	Timeout in seconds for the query

Details

This searches PubChem by SMILES and/or InChI and returns CIDs. The function may work for other output, but this has not been tested. Thanks to Paul Thiessen and Evan Bolton from PubChem team for assistance.

Value

The matching CID

Author(s)

Emma Schymanski <[e-mail]>

References

PubChem search: http://pubchem.ncbi.nlm.nih.gov/

Pubchem REST: https://pubchem.ncbi.nlm.nih.gov/pug_rest/PUG_REST.html

Examples

getPCID.smiles("CC(=O)OC1=CC=CC=C1C(=O)O")

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.