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"""
molvs.cli
~~~~~~~~~
This module contains a command line interface for standardization.
:copyright: Copyright 2016 by Matt Swain.
:license: MIT, see LICENSE file for more details.
*Adapted for purposes of integration of MolVS into RDKit
"""
import argparse
import logging
import sys
from rdkit import Chem
from rdkit.Chem.MolStandardize import Standardizer, Validator
log = logging.getLogger(__name__)
FILETYPES = ['smi', 'mol', 'sdf']
class MolvsParser(argparse.ArgumentParser):
def error(self, message):
sys.stderr.write('Error: %s\n\n'.encode() % message)
self.print_help()
sys.exit(2)
def _read_mol(args):
if args.smiles:
return Chem.MolFromSmiles(args.smiles)
elif args.intype in {'smi', 'smiles'
} or args.infile.name.endswith('smi') or args.infile.name.endswith('smiles'):
return Chem.MolFromSmiles(args.infile.read())
elif args.intype in {'mol', 'sdf'
} or args.infile.name.endswith('mol') or args.infile.name.endswith('sdf'):
return Chem.MolFromMolBlock(args.infile.read())
else:
return Chem.MolFromSmiles(args.infile.read())
def _write_mol(mol, args):
if args.outtype in {
'smi', 'smiles'
} or args.outfile.name.endswith('smi') or args.outfile.name.endswith('smiles'):
args.outfile.write(Chem.MolToSmiles(mol))
args.outfile.write('\n')
elif args.outtype in {'mol', 'sdf'
} or args.outfile.name.endswith('mol') or args.outfile.name.endswith('sdf'):
args.outfile.write(Chem.MolToMolBlock(mol))
else:
args.outfile.write(Chem.MolToSmiles(mol))
args.outfile.write('\n')
def standardize_main(args):
mol = _read_mol(args)
s = Standardizer()
mol = s.standardize(mol)
_write_mol(mol, args)
def validate_main(args):
mol = _read_mol(args)
v = Validator()
logs = v.validate(mol)
for log in logs:
args.outfile.write(log)
args.outfile.write('\n')
if __name__ == '__main__':
"""Main function for molvs command line interface."""
# Root options
# parser = MolvsParser(epilog='use "molvs <command> -h" to show help for a specific command')
parser = MolvsParser(usage="usage: python cli.py [-h] {standardize,validate} ...")
subparsers = parser.add_subparsers(title='Available commands')
# Options common to all commands
common_parser = MolvsParser(add_help=False)
common_parser.add_argument('infile', nargs='?', help='input filename',
type=argparse.FileType('r'), default=sys.stdin)
common_parser.add_argument('-i', '--intype', help='input filetype', choices=FILETYPES)
common_parser.add_argument('-:', '--smiles', help='input SMILES instead of file',
metavar='<smiles>')
common_parser.add_argument('-O', '--outfile', help='output filename', type=argparse.FileType('w'),
default=sys.stdout, metavar='<outfile>')
# Standardize options
standardize_parser = subparsers.add_parser('standardize', help='standardize a molecule',
parents=[common_parser])
standardize_parser.add_argument('-o', '--outtype', help='output filetype', choices=FILETYPES)
standardize_parser.set_defaults(func=standardize_main)
# Validate options
validate_parser = subparsers.add_parser('validate', help='validate a molecule',
parents=[common_parser])
validate_parser.set_defaults(func=validate_main)
args = parser.parse_args()
try:
args.func(args)
except Exception as e:
sys.stderr.write('Error: %s\n\n'.encode() % e.message)
parser.print_help()
sys.exit(2)
|
