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?
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?
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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