RunBioTransformer: RunBioTransformer

In JustinZZW/ImmsTools: Some tools for ion mobility mass spectrometry data processing

Description

R interface to run BioTransformer in CMD. Please refer Djoumbou-Feunang Y, Fiamoncini J, de la Fuente AG, Manach C, Greiner R, and Wishart DS; BioTransformer: A Comprehensive Computational Tool for Small Molecule Metabolism Prediction and Metabolite Identification; Journal of Cheminformatics 201911:2; DOI: 10.1186/s13321-018-0324-5.

Usage

RunBioTransformer(pgm_path, smiles, output_file, task = c("pred", "cid"),
  bt_type = c("ecbased", "cyp450", "phaseII", "hgut", "superbio",
  "allHuman", "envimicro"), str_type = c("-ismi"),
  output_format = c("-ocsv"), n_step = 1)

Arguments

pgm_path	the path of biotransformer program. Default: 'I:/software/Tools/BioTransformer-master'
smiles	the smiles of structure
output_file	the csv name of output
task	'pred', 'cid'. prediction or compound identification. Default: pred
bt_type	'ecbased', 'cyp450', 'phaseII', 'hgut', 'superbio', 'allHuman', 'envimicro'. Default: 'ecbased'. Ref: https://github.com/JustinZZW/BioTransformer
str_type	Default: '-ismi'
output_format	Default: '-ocsv'
n_step	number for reaction. Default: 1

Author(s)

Zhiwei Zhou

Examples

RunBioTransformer(pgm_path='I:/software/Tools/BioTransformer-master',
smiles = "CC(C)C1=CC=C(C)C=C1O",
output_file='I:/software/Tools/BioTransformer-master/test.csv',
n_step=1)

JustinZZW/ImmsTools documentation built on July 9, 2019, 9:32 a.m.