[Rdkit-discuss] comparing two or more tables of molecules

[Stephen O'h. <SO...@ma...>]

Has anyone come up with fool-proof way of matching structurally equivalent molecules?

Unique Smiles or InChI String comparisons don't appear to work presumable because there are different but equivalent structures, e.g. explicit vs non-explicit H's, Kekule vs Aromatic, isomeric forms vs non-isomeric form, tautomers etc.

I also expect that comparing InChI strings might need something more than just a simple string comparison, such as masking off stereo information when you don't care about stereo isomers.

I assume there are suitable tools within RDKit that can do this?

N.B. I need to collate tables from several sources that have a mix of smiles / InChI / sdf molecular representations.

I usually use RDKit via Python and/or Knime.

Cheers,
Steve.