addMissingInChIKeys.CSV: Fill in Missing InChIKeys in CSV files

In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description

This is a small wrapper function to patch CSV files that are missing some InChIKey entries, using Cactus then Open Babel to fill gaps from SMILES.

Usage

addMissingInChIKeys.CSV(csv_file, inchikey_col_number, smiles_col_number, babel_dir, write=TRUE, csv_file_out="")

Arguments

csv_file	Full path and file name to CSV file to fill in InChIKey gaps
inchikey_col_number	Column number of the column containing InChIKeys to check/fill
smiles_col_number	Column number of the SMILES code needed to calculate missing InChIKeys
babel_dir	Path to the directory containing obabel.exe, e.g. "C:/Program Files (x86)/OpenBabel-2.3.2"
write	If TRUE, writes either to csv_file_out (of defined) or overwrites csv_file and returns the file name. If FALSE, returns a list of InChIKeys and does not write to file.
csv_file_out	Full path and file name of output CSV, define to avoid overwriting the original file.

Value

Returns path and file name to CSV file with fixed entries (if necessary) or list of InChIKeys.

Author(s)

Emma Schymanski <[e-mail]>

See Also

getInChIKey.obabel, getCactus, InChIKey_test

Examples

testCSV <- system.file("extdata","CompToxBatchSearch_MetFrag_MSready_C10H14N2_wSelectMetaData.csv",package="ReSOLUTION")
babel_dir <- "C:/Program Files (x86)/OpenBabel-2.3.2"
InChIKeys <- addMissingInChIKeys.CSV(testCSV,13,5,babel_dir,write=FALSE)

schymane/ReSOLUTION documentation built on May 22, 2021, 3:41 a.m.