Open DrrDom opened 2 years ago
The patterns were taken directly from ChEMBL with a few tweaks to make them work with the RDKit. One day, when I get some time, I'll do some curation. I'd be happy to accept PRs from others who can improve the pattern.
I started to play with different filters and found that many compounds were rejected by some of them and started to investigate the cases. One example is Filter82_pyridinium rule (
[c,n]1[c,n][c,n][c,n][c,n]n(C)1
) from Inpharmatica set. RDKit aromatizes some compounds like in example below even with AROMATICITY_SIMPLE model. This results in matching the SMARTS pattern, what I consider a false positive result. The question is whether it was expected that this pattern should remove all such compounds or this should be relevant only for compounds with charged nitrogen ([c,n]1[c,n][c,n][c,n][c,n][n+](C)1
)? Or there could be another workaround? Or this is more rdkit aromaticity model issue?output