Hi,
I've been doing speed comparisons between Daylight and the 2012.06 release of
RDKit for fingerprint calculations. The calculation of a 4179 x 4179 Tanimoto
similarity matrix takes 10 s in DL and 15 s in RDKit. Thus, the new RDKit
release is much improved in terms of speed, although is still slower than DL
(by a 1.5 factor).
The generation of the fingerprints themselves is about 10 times slower: 4s in
DL and 42 s in RDKit.
Thanks,
Gonzalo
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