[Cdk-devel] fingerprint not matching properly (and likely aromaticity problem)

[Rajarshi G. <raj...@gm...>]

Hi, I have the following SMILES strings:
CC(C)(C)N1C2=C(C=N1)C(=O)N(C=N2)CC(=O)NCC3=CC=CC=CC and
O=C(CN1C=NC=CC1=O)NCC2=CC=CC=C2

When I generate fingerprints for these two and test that the second is
a subset of the first, I get false. (Note that before fingerprinting I
detect aromaticity and do atom typing). I also checked SMARTS matching
and that also fails - even when I supply aromatized forms of both
structures.

Can somebody confirm this?

-- 
Rajarshi Guha
NIH Chemical Genomics Center