#!/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,
)
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
