better sanitize handling in read_sdf

[hadim]

Checklist:

• Add tests to cover the fixed bug(s) or the new introduced feature(s) (if appropriate).
• Added a news entry.
  • copy news/TEMPLATE.rst to news/my-feature-or-branch.rst) and edit it.

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Calling dm.sanitize_mol delete the conformers which should not happens by default since you often want the 3d structure when you read an SDF file.

(bug spotted while running unit tests on berth with a recent version of datamol)

[hadim]

Note that this PR restore the original behaviour in 0.3.7. (in that sense 0.3.8 is backward incompatible).

[hadim]

It's tricky to copy/paste the conformers in sanitize_mol because of mol = to_mol(dm.to_smiles(mol), sanitize=True) that very often modify the order of the atoms.

I could map the atoms but I am afraid it would be a bit CPU intensive for what it is.

I also tried using cxsmiles=True but it only conserves the first conformer :-(

[hadim]

I don't see any other way than using the rdkit sanitize flag and discard the use of dm.sanitize_mol in dm.read_sdf. dm.sanitize_mol will be able to copy props but not conformers (and we should trigger a warning message when a conformer is detected).

If you have a better idea, let me know!

[hadim]

Or we could make mol = to_mol(dm.to_smiles(mol), sanitize=True) optional in dm.sanitize_mol.

[maclandrol]

I don't see any other way than using the rdkit sanitize flag and discard the use of dm.sanitize_mol in dm.read_sdf. dm.sanitize_mol will be able to copy props but not conformers (and we should trigger a warning message when a conformer is detected).

Sanitizing with rdkit is probably the better idea, then let the user call dm.sanitize_mol himself if he needs it.

[hadim]

I also tried using cxsmiles=True but it only conserves the first conformer :-(

I just realized that an SDF file can only have one single conformer per molecule, meaning the cxsmiles approach should be fine. That being said I think I prefer to stick to the sanitize from rdkit as said in your last message.

Plan is:

• remove dm.sanitize_mol from dm.read_sdf and use rdkit sanitize.
• copy props in dm.sanitize_mol
• add the cxsmiles trick in sanitize_mol to preserve the first conformer (could be useful) and trigger a warning when more than one conformer is detected.

[maclandrol]

I am perso fine with the current version.

[hadim]

Thanks for the review!