getChemicalProperties: Returns chemical properties given a metabolite list

In ncats/RaMP-DB: RaMP (Relational Database of Metabolomic Pathways)

Returns chemical properties given a metabolite list

Description

Returns chemical properties given a metabolite list

Usage

getChemicalProperties(mets, propertyList = "all", db = RaMP())

Arguments

mets	a list object of source prepended metabolite ids, representing a metabolite set of interest
propertyList	an optional list of specific properties to extract. Options include 'all' (default), 'smiles', 'inchi_key', 'inchi_key_prefix', 'inchi', 'mw', 'monoisotop_mass', 'formula', 'common_name'. If a props list is not supplied, all property fields will be returned.
db	a RaMP database object

Value

Returns chemical property information for the list of input metabolites and a query report reporting on the number of metabolite ids that were matched and the list of un-matched input ids.

The returned object (return_obj below) contains two results. Use str(return_obj) to see the structure described here.

return_obj$chem_props chemical properties for all matched input ids.

return_obj$query_report this reports on the query list size, the number of input ids that were found in the database, and a list of metabolite ids that were not found in the database.

Examples

## Not run: 
# metabolite list of interest
metabolites.of.interest = c("pubchem:64969",
                             "chebi:16958",
                             "chemspider:20549",
                             "kegg:C05598",
                             "chemspider:388809",
                             "pubchem:53861142",
                             "hmdb:HMDB0001138",
                             "hmdb:HMDB0029412")

chemical.classes <- getChemicalProperties(mets = metabolites.of.interest, db = rampDB)

## End(Not run)

ncats/RaMP-DB documentation built on June 10, 2025, 10:50 a.m.