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Fix Issue #22 #33

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Fix Issue #22 #33

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64caf36
remove spurious --sdf
RMeli Mar 1, 2022
f4ba0f1
use output_format, default to sdf
RMeli Mar 1, 2022
ad32327
small improvements
RMeli Mar 1, 2022
b00326a
squeeze in some readme typo fixes
RMeli Mar 1, 2022
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13 changes: 7 additions & 6 deletions xyz2mol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -747,9 +747,6 @@ def main():

parser = argparse.ArgumentParser(usage='%(prog)s [options] molecule.xyz')
parser.add_argument('structure', metavar='structure', type=str)
parser.add_argument('-s', '--sdf',
action="store_true",
help="Dump sdf file")
parser.add_argument('--ignore-chiral',
action="store_true",
help="Ignore chiral centers")
Expand All @@ -768,7 +765,9 @@ def main():
parser.add_argument('-o', '--output-format',
action="store",
type=str,
help="Output format [smiles,sdf] (default=sdf)")
default="sdf",
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Not sure what the intended default behaviour is since the previous options where pointing in opposite directions... SDF or SMILES?

choices=["sdf", "smiles", "smi"],
help="Output format")
parser.add_argument('-c', '--charge',
action="store",
metavar="int",
Expand Down Expand Up @@ -815,11 +814,13 @@ def main():
if args.output_format == "sdf":
txt = Chem.MolToMolBlock(mol)
print(txt)

else:
elif args.output_format in ["smiles", "smi"]:
# Canonical hack
isomeric_smiles = not args.ignore_chiral
smiles = Chem.MolToSmiles(mol, isomericSmiles=isomeric_smiles)
m = Chem.MolFromSmiles(smiles)
smiles = Chem.MolToSmiles(m, isomericSmiles=isomeric_smiles)
print(smiles)
else:
# This should never happen if parser's choices are set correctly
raise ValueError(f"Unsupported output format: {args.output_format}")