NotImplementedError in OBMoleculeSetup.get_equivalent_atoms()

[avnikonenko]

Dear authors, I tried to convert molecule from smiles to pdbqt format, but the new version of Meeko returns error (old version worked correctly) - File "site-packages/meeko/setup.py", line 698, in get_equivalent_atoms raise NotImplementedError NotImplementedError version of the packages: numpy 1.20.3 scipy 1.6.2 rdkit 2021.03.5 meeko 0.3.0 code:

smi = 'O=C(C)Oc1ccccc1C(=O)O'

mol = Chem.MolFromSmiles(smi)
mol = Chem.AddHs(mol, addCoords=True)
params = AllChem.ETKDGv3()
params.useRandomCoords = False
params.randomSeed = 120
AllChem.EmbedMolecule(mol, params)
AllChem.UFFOptimizeMolecule(mol, maxIters=100)
molecule_sdf = Chem.MolToMolBlock(mol)

mol = obutils.load_molecule_from_string(molecule_sdf, molecule_format='SDF')

mol.AddHydrogens()
charge_model = ob.OBChargeModel.FindType("Gasteiger")
charge_model.ComputeCharges(mol)

preparator = MoleculePreparation(keep_nonpolar_hydrogens=False,
                                 hydrate=False, flexible_amides=False,
                                 rigid_macrocycles=False, min_ring_size=7, max_ring_size=33,
                                 rigidify_bonds_smarts=[], rigidify_bonds_indices=[],
                                 double_bond_penalty=50, atom_type_smarts={},
                                 is_protein_sidechain=False, add_index_map=False,
                                 stop_at_defaults=False, remove_smiles=False)
preparator.prepare(mol)

Could you help me please? Thank you!

[diogomart]

Hi,

You should pass the RDKit molecule to preparator.prepare() instead of passing the OpenBabel Molecule. In your script, delete the following lines:

molecule_sdf = Chem.MolToMolBlock(mol)

mol = obutils.load_molecule_from_string(molecule_sdf, molecule_format='SDF')

mol.AddHydrogens()
charge_model = ob.OBChargeModel.FindType("Gasteiger")
charge_model.ComputeCharges(mol)

The reason is that Meeko is now using RDKit instead of OpenBabel. However, we still kept OpenBabel around and in case we want to go back to it, but there's one function that we didn't implement yet in the OpenBabel side of the code, hence the NotImplementedError.

Best regards,

[avnikonenko]

Thank you!