doBT: Run Biotransformer on SMILES.

In MetaDBparse: Annotate Mass over Charge Values with Databases and Formula Prediction

Description

To predict enzymatic metabolite changes, you can enable Biotransformer processing in the base database creation. This runs the process on a given SMILES string.

Usage

doBT(
  smis = c("CCNC1=NC(=NC(=N1)Cl)NC(C)C"),
  jarloc,
  opts = "cyp450:2; phaseII:1",
  cl = 0,
  help = FALSE
)

Arguments

smis	SMILES string character vector
jarloc	Location of Biotransformer .jar file.
opts	-q command line options.
cl	parallel::makeCluster object.
help	Show help for opts only?

Value

Data table with metabolites of given SMILES and which reaction it pertains.

See Also

fread,rbindlist pblapply

Examples

## Not run: myFolder = tempdir()
## Not run: btLoc = downloadBT(outfolder = myFolder)
## Not run: doBT(smis = c("CCNC1=NC(=NC(=N1)Cl)NC(C)C"),
     jarloc = btLoc,
     opts = "cyp450:2; phaseII:1")
## End(Not run)

MetaDBparse documentation built on May 3, 2021, 5:09 p.m.