On 5 November 2010 22:20, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >> For interest I tested Open Babel using Rich's substructure benchmark >> at >> http://depth-first.com/articles/2009/01/22/mx-performance-comparison-3-substructure-search-in-mx-and-cdk/. >> My code is at https://gist.github.com/663914. > > Would you try running the benchmark with Chris's implicit valence > adjustments? (The one which changes the IMPVAL to not require hybridization > SMARTS.) > > I'm curious how much of a hit the hybridization assignment causes.
Well, before I do that, I took a shortcut - I just ran the search a second time. If the hybridization was taking time, then the second search should be much faster. In fact, it took almost exactly the same time. (Now it may be that the assignment is still taking place behind the scenes with a copy of the molecule or something - I might check this out). The second point to make is that Tim's implementation is not optimal for substructure searching, but for isomorphisms (if I understood Tim correctly). We expect Vflib to do better than Nauty for substructures. > Thanks, > -Geoff > ------------------------------------------------------------------------------ > The Next 800 Companies to Lead America's Growth: New Video Whitepaper > David G. Thomson, author of the best-selling book "Blueprint to a > Billion" shares his insights and actions to help propel your > business during the next growth cycle. Listen Now! > http://p.sf.net/sfu/SAP-dev2dev > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
