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sdf_title2field.py
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sdf_title2field.py
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#!/usr/bin/env python
#==============================================================================
# author : Pavel Polishchuk
# date : 01-11-2014
# version : 0.1
# python_version : 3.2
# copyright : Pavel Polishchuk 2014
# license : GPL3
#==============================================================================
import argparse
import sys
from rdkit import Chem
def main_params(in_fname, out_fname, field_name, force):
w = Chem.SDWriter(out_fname)
w.SetKekulize(False)
for m in Chem.SDMolSupplier(in_fname, False, False, False):
if m:
if m.HasProp(field_name) and not force:
sys.stderr.write(f'The field {field_name} exists. If you want to overwrite it please use --force '
f'argument\n')
exit()
m.SetProp(field_name, m.GetProp('_Name'))
w.write(m)
w.close()
def main():
parser = argparse.ArgumentParser(description='Extract field values from sdf-files.')
parser.add_argument('-i', '--input', metavar='FILENAME', required=True,
help='input SDF file, molecules should have titles')
parser.add_argument('-o', '--output', metavar='FILENAME', required=True,
help='output SDF file')
parser.add_argument('-f', '--field_name', metavar='STRING', required=True,
help='field name where to insert molecule title. If the field exists, the script will be '
'interrupted.')
parser.add_argument('--force', action='store_true', default=False,
help='force to overwrite existing field name.')
args = parser.parse_args()
main_params(args.input, args.output, args.field_name, args.force)
if __name__ == '__main__':
main()