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goraj/rdkit_iron.py

Created October 24, 2019 17:17
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rdkit_iron.py
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rdkit_iron.py
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
# works
smiles_charged = '[CH2-][Fe++][CH2-]'
# does not work
smiles_charged = 'CCCC(=O)c1ccc[c-]1[Fe++][c-]1cccc1C(=O)CCC'
smiles_charged = 'Cc1ccc(C(=O)C=Cc2ccc[c-]2[Fe++][c-]2cccc2)c(O)c1'
print(f'smiles_uncharged: {smiles_charged}')
mol = Chem.MolFromSmiles(smiles_charged)
uncharger = rdMolStandardize.Uncharger()
mol_uncharged = uncharger.uncharge(mol)
smiles_uncharged = Chem.MolToSmiles(mol_uncharged)
print(f'smiles_uncharged: {smiles_uncharged}')
assert Chem.MolFromSmiles(smiles_uncharged) != None
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