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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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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ Depends on `rdkit`, `numpy`, and `networkx`. Easiest to setup via anaconda/conda

`conda install -c conda-forge xyz2mol`

Setup for a standalone enviroment is avaliable via `Makefile`. To setup and test simply clone the project and make.
Setup for a standalone environment is available via `Makefile`. To setup and test simply clone the project and make.

git clone https://github.com/jensengroup/xyz2mol

Expand All @@ -31,7 +31,7 @@ Note, it is also possible to run the code without the `networkx` dependencies, b

## Example usage

Read in xyz file and print out the SMILES, but don't incode the chirality.
Read in xyz file and print out the SMILES, but don't encode the chirality.

xyz2mol.py examples/chiral_stereo_test.xyz --ignore-chiral

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13 changes: 7 additions & 6 deletions xyz2mol.py
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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}")