From: Thomas S. <beg...@ho...> - 2010-11-30 19:58:42
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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 ------------------------------------------------------------------------------ Increase Visibility of Your 3D Game App & Earn a Chance To Win $500! Tap into the largest installed PC base & get more eyes on your game by optimizing for Intel(R) Graphics Technology. Get started today with the Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs. http://p.sf.net/sfu/intelisp-dev2dev _______________________________________________ Cdk-user mailing list Cdk...@li... https://lists.sourceforge.net/lists/listinfo/cdk-user |