Add SMILES-derived structural features to a metabolite database

Add SMILES-derived structural features to a metabolite database

Usage

AnnotateSMILESStructure(
  db,
  smiles_column = NULL,
  backend = c("auto", "native"),
  overwrite = FALSE,
  strict = FALSE,
  workers = getOption("SpaMTP.smiles_workers", 1L)
)

Arguments

db

A metabolite data frame.

smiles_column

Column containing SMILES. When NULL, SpaMTP detects iso_smiles, canonical_smiles, or smiles.

backend

Parser backend passed to DeconvolveSMILES().

overwrite

Replace existing feature values. By default only absent or missing values are filled.

strict

Passed to DeconvolveSMILES().

workers

Parallel workers passed to DeconvolveSMILES().

Value

db with structure-derived columns appended or completed.

Examples

utils::str(formals(AnnotateSMILESStructure))
#> Dotted pair list of 6
#>  $ db           : symbol 
#>  $ smiles_column: NULL
#>  $ backend      : language c("auto", "native")
#>  $ overwrite    : logi FALSE
#>  $ strict       : logi FALSE
#>  $ workers      : language getOption("SpaMTP.smiles_workers", 1L)