getSmilesInchi: getSmilesInchi

In RAMClustR: Mass Spectrometry Metabolomics Feature Clustering and Interpretation

getSmilesInchi

Description

use PubChem API to look up full smiles and inchi notation for each inchikey

Usage

getSmilesInchi(ramclustObj = NULL, inchikey = NULL, ignore.stereo = TRUE)

Arguments

ramclustObj	ramclustR object to look up smiles and inchi for each inchikey (without a smiles/inchi). Must provide one of ramclustObj or inchikey.
inchikey	character vector of inchikey strings. Must provide one of ramclustObj or inchikey.
ignore.stereo	logical. default = TRUE. If the Pubchem databases does not have the full inchikey string, should we search by the first (non-stereo) block of the inchikey? When true, returns the first pubchem match to the inchikey block one string. If the full inchikey is present, that is used preferentially.

Details

The $inchikey slot is used to look up parameters from pubchem. PubChem CID, a pubchem URL, smiles (canonical) and inchi are returned. if smiles and inchi slots are alread present (from MSFinder, for example) pubchem smiles and inchi are used to fill in missing values only, not replace.

Value

returns a ramclustR object. new vector of $smiles and $inchi with length equal to number of compounds.

Author(s)

Corey Broeckling

References

Kim S, Thiessen PA, Bolton EE, Bryant SH. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem. Nucleic Acids Res. 2015;43(W1):W605-11.

RAMClustR documentation built on Oct. 20, 2023, 5:08 p.m.