searchSim: PubChem Similarity (Fingerprint) Search

In girke-lab/ChemmineR: Cheminformatics Toolkit for R

PubChem Similarity (Fingerprint) Search

Description

Accepts one SDFset container and performs a >0.9 similarity PubChem fingerprint search, returning up to 200 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. If the input object contains multiple items, only the first is used as a query.

Usage

searchSim(sdf)

Arguments

sdf	A SDFset object which contains one compound

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: 
## get a sample compound
data(sdfsample); sdfset <- sdfsample[2]
## search a compound on PubChem
compounds <- searchSim(sdfset)
## End(Not run)

girke-lab/ChemmineR documentation built on July 28, 2023, 10:36 a.m.