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paconius avatar paconius commented on July 25, 2024

Okay. I've looked into this a bit more and the root cause is that the rdkit cartridge does not allow anything other than SMILES to be used in queries. Therefore it appears that a big chunk of the fields.py code is not correct as it tries to feed mol objects to queries when only SMILES would be accepted.

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rvianello avatar rvianello commented on July 25, 2024

thank you for the report, I'll have a look into this and I'll try to post some additional comments.

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paconius avatar paconius commented on July 25, 2024

After more digging, I was wrong -- the cartridge does allow pickled mol objects to be used in queries. The issue was that the current MolField functions weren't properly pickling them. I've got it working now by modifying the picking of objects.

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rvianello avatar rvianello commented on July 25, 2024

Thank you for submitting a PR, I was just about to suggest it. I'd leave this issue open until the PR is merged, if ok for you.

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paconius avatar paconius commented on July 25, 2024

Took awhile to get it working for all tests. After all that the key issue was a missing "mol_from_pkl" inside get_prep_value().

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rvianello avatar rvianello commented on July 25, 2024

Thank you the new version of the PR is not only more compact, but it also makes the intent clearer (and it fixes the tests, which was indeed an issue). I'll probably have a closer look at it again later today.

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