The current PubChem Fingerprints are not implemented correctly. The implementation is using SSSR when it should be using ESSSR for the ring perceptions. From the forth page of the [Specifications/Section 2]:(ftp://ftp.ncbi.nlm.nih.gov/pubchem/specifications/pubchem_fingerprints.pdf)
Rings in a canonic Extended Smallest Set of Smallest Rings
(ESSSR) ring set - These bits test for the presence or
count of the described chemical ring system. An ESSSR ring
is any ring which does not share three consecutive atoms
with any other ring in the chemical structure. For
example, naphthalene has three ESSSR rings (two phenyl
fragments and the 10-membered envelope), while biphenyl
will yield a count of only two ESSSR rings.
More info on the KNIME forum:
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