Re: [Cdk-user] comment about VF2 implementation from chemkit - possible bug

[Nina J. <jel...@gm...>]

On 8 September 2011 12:24, Joos Kiener <jo...@su...> wrote:

> 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.
>
>
Just to note a comparison between a library method (as UIT) to a database
search is not quite fair, as database search systems usually employ lot of
pre-screening and other optimization techniques.

e.g. this online search does use CDK ( but not UIT )

http://apps.ideaconsult.net:8080/ambit2/query/smarts?type=smiles&search=CCC%28C%28CC%28C%28C%29C%29C%29C%29C&text=&page=0&pagesize=100


Best regards,
Nina


> 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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