Hi all,
first off i guess you will be hearing more from me rather sooner than later
but now to the actually subject. Please see:
http://chembioinfo.wordpress.com/2011/03/15/benchmarking-substructure-search/
for the context of this message.
Currently I'm playing around with substructure search ( I have a certain
goal in mind, more on that in later messages). Anyway UIT isn't exactly fast
especially compared to commercial products like ChemFinder or InstantJChem
were searches seem almost instantaneous.
I was comparing UIT and the above referenced code ported from chemkit. First
the difference in real world usage seems much less extreme than in that
benchmark (for small molecules) or I'm misinterpreting the chart. Anyway in
my case it takes about 60% of the time compared to UIT.
Now to the subject of the message. I think there is an issue in the ported
version. Following query returns 44 hits with chemkit and 106 with UIT.
ChemFinder also gives 106 hits so I'm inclined to believe 106 is correct.
Here the Query Molecule:
CCC(C(CC(C(C)C)C)C)C
Did not find or check for any other inconsistencies.
Best Regards,
Joos Kiener
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