TypeError: in method 'new_OBMol'

[ichxw]

I got an error when trying to run the following lines:

import oddt
from rdkit import Chem
from rdkit.Chem import AllChem
smi = 'c1ccccc1NCC(=O)OCCCC'
mol = Chem.MolFromSmiles(smi)
mol = Chem.AddHs(mol)
AllChem.EmbedMultipleConfs(mol, numConfs = 1, numThreads = 1, randomSeed=42)
mol = oddt.toolkit.Molecule(mol)
mol_conf = oddt.toolkits.rdk.diverse_conformers_generator(mol, n_conf=10, method='etkdg', seed=42, rmsd=0.2)

The error message was:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/xzhu/.conda/envs/my-rdkit-env/lib/python3.8/site-packages/oddt/toolkits/rdk.py", line 1217, in diverse_conformers_generator
    mol_clone = mol.clone
  File "/home/xzhu/.conda/envs/my-rdkit-env/lib/python3.8/site-packages/oddt/toolkits/ob.py", line 407, in clone
    return Molecule(ob.OBMol(self.OBMol))
  File "/home/xzhu/.conda/envs/my-rdkit-env/lib/python3.8/site-packages/openbabel/openbabel.py", line 2273, in __init__
    _openbabel.OBMol_swiginit(self, _openbabel.new_OBMol(*args))
TypeError: in method 'new_OBMol', argument 1 of type 'OpenBabel::OBMol const &'
Additional information:
Wrong number or type of arguments for overloaded function 'new_OBMol'.
  Possible C/C++ prototypes are:
    OpenBabel::OBMol::OBMol()
    OpenBabel::OBMol::OBMol(OpenBabel::OBMol const &)

I ran them in python 3.8 on Ubuntu 22.04.1 LTS (GNU/Linux 5.15.0-52-generic x86_64). Below are version of some libraries.

>>> babel.__version__
'2.11.0'
>>> rdkit.__version__
'2021.03.1b1'
>>> oddt.__version__
'0.7'

What could be the possible reasons?
Thank you.

[mwojcikowski]

You should be using RDKit flavor of oddt's Molecule. The following change will fix the code.

...
mol = oddt.toolkits.rdk.Molecule(mol)
...

[ichxw]

Got it. Thanks a lot.