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Description
Description:
The following code to generate conformers using datamol works fine with RDKit version 2022.09.5, but fails with RDKit version 2024.03.1. This inconsistency might be due to changes in RDKit which datamol has not yet adapted to.
Versions:
datamol: 0.12.4rdkit: 2022.09.5 (works fine)rdkit: 2024.03.1 (raises error)
Reproducible Code:
import datamol as dm
smiles = "[H]/C1=C(\\[H])C([H])([H])/N=C(\\[H])OC([H])([H])C1=O"
mol = dm.to_mol(smiles)
mol = dm.conformers.generate(mol, align_conformers=True, add_hs=True, n_confs=10)
mol = dm.add_hs(mol, add_coords=True)Error Traceback:
ValueError Traceback (most recent call last)
Cell In[9], line 5
3 smiles = "[H]/C1=C(\\[H])C([H])([H])/N=C(\\[H])OC([H])([H])C1=O"
4 mol = dm.to_mol(smiles)
----> 5 mol = dm.conformers.generate(mol, align_conformers=True, add_hs=True, n_confs=10, method='ETKDG')
6 mol = dm.add_hs(mol, add_coords=True)
File ~/.conda/envs/chem/lib/python3.11/site-packages/datamol/conformers/_conformers.py:171, in generate(mol, n_confs, use_random_coords, enforce_chirality, num_threads, rms_cutoff, clear_existing, align_conformers, minimize_energy, sort_by_energy, method, forcefield, ewindow, eratio, energy_iterations, warning_not_converged, random_seed, add_hs, ignore_failure, embed_params, verbose)
167 logger.warning(
168 f"Conformers embedding failed for {convert.to_smiles(mol)}. Returning None because ignore_failure is set."
169 )
170 return None
--> 171 raise ValueError(f"Conformers embedding failed for {convert.to_smiles(mol)}")
173 energies = None
175 # Minimize energy
ValueError: Conformers embedding failed for [H]/C1=N\C([H])([H])/C([H])=C(\[H])C(=O)C([H])([H])O1
Steps to Reproduce:
- Install
datamolversion0.12.4. - Install
rdkitversion2024.03.1. - Run the provided code snippet.
Expected Behavior:
The conformers should be generated without any errors as it works with RDKit version 2022.09.5.
Actual Behavior:
The conformer generation raises a ValueError with RDKit version 2024.03.1.
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