On 25 February 2011 12:30, <ma...@ebi.ac.uk> wrote: > > > > I wonder why I haven't asked this before. How is this done on OrChem? > > > > "These columns provide a quick way to materialize a basic CDK molecule to > > be passed into the VF2 algorithm. The data structures used are quite > > straightforward, for instance with data in column atom "C O" interpreted > > as: "atom 0 is Carbon, atom 1 is Oxygen" and bond > > column "0 1 D Y" then implying "there is a bond between C (atom 0) and O > > (atom 1) that is double (D) and aromatic is true (Y)". In this way, CDK > > molecules can be generated very fast without the need for calculating > > any properties during the search." > > > Yes, 'properties' here means mainly aromaticity, which is relatively > expensive to calculate. So the database molecules get a fingerprint but > they also get stored in a simple format for quick re-assembly before going > into VF2. >
I think it was already mentioned in this thread - store precalculated information for properties , which take long to calculate, e.g. aromaticity and rings, and just load them into the CDK structure before doing the substructure match. > > > > Is this VF2 the turbo-substructure algorithm? Or a custom one? > > It's custom, I still have to see if I can replace it with SMSD and if that > would be faster. At the time the CDK did not offer a VF2 algorithm. > > UIT would do as well. > > Do you create real cdk molecules or just some kind of graph > representation > > you but in your custom VF2? > > The latter, just what I need for VF2. > > > > > Which properties do you need for VF2? Implicit hydrogens? Or is it enough > > to assign an atom it's symbol "C" and each bond an order? > > Element symbol, explicit hydrogens, bond orders, aromaticity. I don't > include charge, I probably should (so now the search is charge > insensitive) > > It's also really beneficial to 'sort' the atom container, it's described > somewhere in the paper. Try and let VF2 match the least common elements > first (generally not the carbons or oxygens). I benchmarked that and > performance shot up. > Mark, is your implementation of VF2 algorithm available for testing? We are doing some benchmarking of isomorphism tester currently and would be interesting to compare VF2 as well. Nina > > cheers, > Mark > > > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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