DB Framework: Type Mapper for Chemistry & Biology + RDKit

Just wanted to ask what the status on this is:

Previous thread was automatically closed and in 4.2 this isn’t yet implemented.

On top of that it would also be great if the DB Nodes would work well with the RDKit cartridge. Namely with GUI tools like pgadmin4 one can insert smiles directly into a “mol” type column. Same is true with GUI tools that use the standard JDBC driver like KNIME does. However KNIME nodes seem to do some explicit type conversions that breaks the rdkit cartridges built-in automatic conversion:

Execute failed: Batch entry 0 INSERT INTO test (“rdkit_mol”) VALUES (‘c1ccccc1’) was aborted: ERROR: column “rdkit_mol” is of type mol but expression is of type character varying

While running a simple insert in a GUI tool works just fine:

INSERT INTO test (rdkit_mol) VALUES (‘c1ccccc1’);

Not sure what exactly is happening here but more flexibility on this type side is needed. Something like override type conversions “send as is”?

Hi @beginner

Thanks a lot for reaching out!
So I have checked with our developers (apologies, this can take a while most of the times):
regarding the writing of mol data via the RDKit cartridge a bug ticket has been opened. You also might check out this post: sdf mol_file type to rdkit mol type

Regarding the chemistry type handling in the DB nodes I added your request to the ticket. As far as I know they encountered unexpected problems with the AdapterCell implementation. So no solution yet, but they’re on it :slight_smile:

Hope I have better news soon!


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