I have been calculating fingerprints for 3000
'real-life' molecules, using the default settings for
the FingerPrinter class (which are not described in the
API JavaDoc - I think they probably should be). Most
molecules took a fraction of a second to calculate.
However, a couple of them took up to 8 hours.
This was due to a large number of subgraphs (I think).
Is there any way to guesstimate whether a particular
molecule will be very slow to FingerPrint, so that it
can be left out of a screen if desired? In the end, it
took around 4 days to calculate fingerprints for the
3000 molecules. To be fair to FingerPrinter, the slow
molecules did not look very drug-like, but I would have
prefered to leave 6 molecules out and complete the
calculation in one hour, rather than include them, and
take 4 days.
If you are interested, I have attached one of the slow
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