File: sdf2smi.py

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rdkit 201809.1%2Bdfsg-6
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import argparse
from rdkit import Chem
from rdkit.Chem.rdmolfiles import SmilesWriter

parser = argparse.ArgumentParser()
parser.add_argument('inputfile', help="sdf filename for convert to smiles")
args = parser.parse_args()
sdf = Chem.SDMolSupplier( args.inputfile )
writer = SmilesWriter("converted.smi")

for mol in sdf:
    writer.write( mol )
writer.close()