#!/usr/bin/env python """ Input: File with tab separated columns. One column contains the id's of a collection of molecules that should to be retrieved. Output: Retrieved compounds """ import argparse import sys import cheminfolib import psycopg2.extras cheminfolib.pybel_stop_logging() def parse_command_line(argv): parser = argparse.ArgumentParser() parser.add_argument( "-i", "--input", required=True, help="input file name containing one or multiple unique molecule identifiers", ) parser.add_argument( "-c", "--column", required=True, type=int, help="#column containing the id codes", )
def start_parser(args): (path, schema, conn_string, molecule_type) = args cheminfolib.pybel_stop_logging() gmp = GenericMoleculeParser(path, schema, conn_string, molecule_type) gmp.parse_into_database() return path
#!/usr/bin/env python """ Input: set of molecules with pre-calculated physico-chemical properties Output: set of molecules that pass all the filters Copyright 2012, Bjoern Gruening and Xavier Lucas TODO: AND/OR conditions? """ import sys, os import argparse import cheminfolib import json import pybel import shlex, subprocess cheminfolib.pybel_stop_logging() def parse_command_line(): parser = argparse.ArgumentParser() parser.add_argument('-i', '--input', help='Input file name') parser.add_argument('-iformat', help='Input file format') parser.add_argument('-oformat', default='smi', help='Output file format') parser.add_argument('-o', '--output', help='Output file name', required=True) parser.add_argument('--filters', help="Specify the filters to apply", required=True, )