Hi,
I have performed a similarity matrix calculation of 4176 X 4016 molecules with
a program using the RDKit and it took 401 seconds. The same program with the
same sets of molecules and using the Daylight toolkit took 19 seconds.
Has anybody observed similar results? The main difference in time seems to come
from the Tanimoto similarity calculation (although the fingerprint generation
is also slower). I'm concerned about the impact in e.g. clustering algorithms
with large datasets.
I used the defaults for fingerprint generation in RDKit. Not sure if something
can be done to improve this.
Thanks a lot,
Gonzalo
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