When doing substructure searches we have noticed an inconsistency which can be exemplified as follows:
If one makes a substructure search with a cyclohexane ring (C6H12) one would expect that the hit-set would include all the structures including this structural feature (six carbons in a ring).
That includes compounds with a benzene ring (C6H6) – but that is not the case. If we search our database for a cyclohexane ring with free substitution we get much fewer hits that if we perform the same search with a benzene-ring and free substitution - it should be the other way around as the hit-set from the benzene ring search (C6H6) should also be included in the cyclohexane-search (C6H12).
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