cleanDB: Uniformize database and remove invalid formulas/SMILES

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

Description

This is a wrapper function to take a 'raw' input data table with compound information, uniformize the SMILES

Usage

cleanDB(db.formatted, cl, silent = TRUE, blocksize, smitype = "Canonical")

Arguments

db.formatted	Data table with columns 'compoundname, structure, baseformula, charge, description'
cl	parallel::makeCluster object for multithreading
silent	Suppress warnings?
blocksize	How many compounds to process per 'block'? Higher number means bigger memory spikes, but faster processing time.
smitype	SMILES format, Default: 'Canonical'

Value

Data table with SMILES in the correct format, and charge/formula re-generated from said SMILES if available.

See Also

clusterApply pbapply check_chemform rbindlist

Examples

## Not run: myDB = build.LMDB(tempdir())
## Not run: cleanedDB = cleanDB(myDB$db, cl = 0, blocksize = 10)

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