splitPFAS.csv: Run SplitPFAS on a CSV file containing SMILES

In schymane/RChemMass: Various Cheminformatic, Curation and Mass Spectrometry Functions

Description

A little wrapper function to run SplitPFAS on a csv file containing SMILES and other fields, optionally running InChIKey checks NOTE: some options only work for very specific files. Use with caution.

Usage

splitPFAS.csv(
  pfas_file,
  splitPFAStools_name,
  smarts_file,
  babel_dir,
  incl_image = TRUE,
  smiles_col_index = 3,
  SMILES_KeyCheck = TRUE,
  func_group_col_index = 5,
  Func_Group_KeyCheck = FALSE,
  pfas_part_col_index = 6,
  PFAS_Part_KeyCheck = FALSE
)

Arguments

pfas_file	Name of the CSV file containing at least one SMILES column
splitPFAStools_name	Name of the SplitPFAS jar. See splitPFAS
smarts_file	Name of the SMARTS file. See splitPFAS
babel_dir	Location of Open Babel dir. Needed for InChIKey checks.
incl_image	Whether to include image generation. See splitPFAS
smiles_col_index	Index of the column containing SMILES. Default 3.
SMILES_KeyCheck	Boolean to indicate if SMILES InChIKey check should be performed.
func_group_col_index	Index of column containing functional group. For validation only.
Func_Group_KeyCheck	Default FALSE. Checks functional group InChIKeys if TRUE - only for test files that contain this information (advanced users only)
pfas_part_col_index	Index of column containing functional group. For validation only.
PFAS_Part_KeyCheck	Default FALSE. Checks functional group InChIKeys if TRUE - only for test files that contain this information (advanced users only).

Details

Returns a csv file containing the SplitPFAS results.

Author(s)

Emma Schymanski <[e-mail]>

See Also

splitPFAS.help, splitPFAS

Examples

pfas_file <- system.file("extdata","PFAS_SplitSmiles_ExamplesExt.csv",package="RChemMass")
splitPFAStools_name <- "MetFrag2.4.5-Tools.jar"
smarts_file <- system.file("extdata","SplitPFAS_smarts.txt",package="RChemMass")
babel_dir <- "C:/Program Files/OpenBabel-2.4.1"
splitPFAS.csv(pfas_file, splitPFAStools_name, smarts_file, babel_dir,
              incl_image = TRUE, smiles_col_index = 3, SMILES_KeyCheck = TRUE,
              func_group_col_index = 5, Func_Group_KeyCheck = FALSE,
              pfas_part_col_index = 6, PFAS_Part_KeyCheck = FALSE)
              
splitPFAS.csv(pfas_file, splitPFAStools_name, smarts_file, babel_dir,
              incl_image = TRUE, smiles_col_index = 3, SMILES_KeyCheck = TRUE,
              func_group_col_index = 5, Func_Group_KeyCheck = TRUE, 
              pfas_part_col_index = 6, PFAS_Part_KeyCheck = TRUE)
              
pfas_file <- system.file("extdata","Fluroseedset_1to30.csv",package="RChemMass")
splitPFAS.csv(pfas_file, splitPFAStools_name, smarts_file, babel_dir,
              incl_image = TRUE, smiles_col_index = 5, SMILES_KeyCheck = TRUE,
              Func_Group_KeyCheck = FALSE, PFAS_Part_KeyCheck = FALSE)
              

schymane/RChemMass documentation built on Jan. 25, 2021, 5:45 a.m.