Short python script for guessing the 3D structure of a molecule from a smiles string and writing out to mol file

smiles_to_mol.py

# smiles_to_mol.py

__doc__ = """Guesses the initial geometry of a molecule based on SMILES string
"""

###############################
from rdkit import Chem
from rdkit.Chem import AllChem
import sys
###############################

# Get parameters
smiles = sys.argv[1]
mol_out = sys.argv[2]

m = Chem.MolFromSmiles(smiles)
m2 = Chem.AddHs(m)

# Generate initial guess
AllChem.EmbedMolecule(m2,AllChem.ETKDG())
AllChem.MMFFOptimizeMolecule(m2)

# Write mol file
print(Chem.MolToMolBlock(m2),file=open(mol_out,'w'))