searchString: PubChem Similarity (Fingerprint) SMILES Search

In girke-lab/ChemmineR-release: Cheminformatics Toolkit for R

Description

Accepts one SMILES string (Simplified Molecular Input Line Entry Specification) and performs a >0.95 similarity PubChem fingerprint search, returning the hits in an SDFset container. The ChemMine Tools web service is used as an intermediate, to translate queries from plain HTTP POST to a PubChem Power User Gateway (PUG) query.

Usage

searchString(smiles)

Arguments

smiles

A character object which contains one SMILES string

Value

SDFset

for details see ?"SDFset-class"

Author(s)

Tyler Backman

References

PubChem PUG SOAP: http://pubchem.ncbi.nlm.nih.gov/pug_soap/pug_soap_help.html

Chemmine web service: http://chemmine.ucr.edu

PubChem help: http://pubchem.ncbi.nlm.nih.gov/search/help_search.html

SMILES Format: http://en.wikipedia.org/wiki/Chemical_file_format#SMILES

Examples

## Not run: 
## search a compound on PubChem
compounds <- searchString("CC(=O)OC1=CC=CC=C1C(=O)O")
## End(Not run)

girke-lab/ChemmineR-release documentation built on May 17, 2019, 5:26 a.m.