The current FP3 and FP4 fingerprints reparse the SMARTS patterns for every fingerprint instead of keeping the patterns around for future use. This would probably improve the overall performance of FP generation.
The relevant code is in fingerprints/finger3.cpp:PatternFP.GetFingerprint
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Not really a bug, but a good suggestion which doesn't look too difficult. I'll tackle it when v2.2.0 release is out of the way.
Chris