Hi Thomas,
On 30 November 2010 21:58, Thomas Strunz <beginn...@hotmail.de> wrote:
> Hi Nina,
>
> I sure have more than 1 IAtomContainer in memory at time so I agree that
> might be an issue but if screening lets say returns 1000 hits, 1000 subgraph
> matches must be done and hence all the 1000 Molecules must be created first.
> So you would suggest to read each one separatley from database after a
> subgraph match returns?
>
What we are doing is getting database structure identifiers from
prescreening and reading structures one by one for subgraph matching. Few
thousand of IAtomContainers is fine for desktop application, but server side
one could have multiple queries at the same time and multiply the thousands
to unreasonable number.
> A second issue is, if the query Molecule is a common fragment in the
> database, let's assume benzene, and llike 80% of the fingerprints match, how
> do you handle that and keep performance? subgraph matches on so mnay
> structures will no perfrom well. How can you prevent that with very common
> substructures?
>
We have several levels of prescreening, fingerprints only are not sufficient
for reasonable performance. Also precalculated aromaticity flags to avoid
calculating that on the fly and caching of the final results. You could get
an overview from this poster from QSAR2010
http://www.ideaconsult.net/downloads/rhodes/posters/SMARTS.pdf .
Regards,
Nina
>
> Regards,
>
> Thomas
>
>
>
> Just my two cents.
>
> Besides prescreening, having minimum IAtomContainer objects in memory is
> the key to performance. As less than one object doesn't make sense :) one
> IATomContainer at a time is the best. Fingerprints can be pre-calculated
> and no need to be loaded in-memory at all, let SQL do the prescreening.
>
> We've been doing similar things (CDK, relational database, no cartridges)
> in ambit (ambit.sourceforge.net) for quite few years already. There is
> downloadable standalone application and a servlet container application war
> file (to run your own service), as well as a running OpenTox REST services
> for substructure searching , e.g.
>
>
> https://ambit.uni-plovdiv.bg:8443/ambit2/query/smarts?search=c1ccccc1[Cl,Br,F]
>
>
> http://apps.ideaconsult.net:8080/ambit2/query/smarts?search=c1ccccc1[Cl,Br,F,I]
>
> Regards,
> Nina
>
>
> Regards,
>
> Thomas
>
>
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