It seems my message didn't go through, thus resending it in plain text.
It's an aromaticity question again. The attached file contains two
records, two representations of Benzo(k)fluoranthene - one Kekule and
one aromatic, with aromatic bonds represented with SDF bond order 4.
After reading and all preprocessing, in the first (Kekule) structure
all but two bonds are aromatic, while in the second structure, all
bonds are aromatics.
Both structures generate the same SMILES c1ccc2cc3c5cccc4cccc(c3(cc2(c1)))c45.
However, the difference in bonds flags in the 5-membered ring, results
in quite different fingerprints by any of
PubchemFingerprinter, MACCSFingerprinter and EStateFingerprinter.
What should be the correct behaviour ? Is the aromaticity detection
or SMILES generation wrong?