Hi, After a quick look at the UIT code, it does seem quite efficient, yes. It uses the same atomcontainer instances passed in, uses BitSets, &ct.
However I would disagree slightly about one thing; this code : IAtomContainer copyAtomContainer = builder.newInstance(IAtomContainer.class, atomContainer); does have an effect - it removes null references. In other words, it is possible to have atomContainers where some of the refs in the atoms array are null. Copying in this way will - I think - 'clean' the atomcontainer of nulls. I haven't tested this, but I have run into bugs before due to this situation. I'm not saying it couldn't be done better, of course. I would also be interested in speed comparisons between UIT/SMSD, by the way. gilleain On Tue, Mar 1, 2011 at 9:37 AM, Egon Willighagen <egon.willigha...@gmail.com> wrote: > Nina, > > On Tue, Mar 1, 2011 at 9:58 AM, Nina Jeliazkova > <jeliazkova.n...@gmail.com> wrote: >> To share a bit of our recent benchmarking experience, we actually found CDK >> UIT is faster than SMSD for substructure searching (haven't tested MCSS). > > If not CDK News, you should consider http://figshare.com/ for those > benchmark result plots, as a micropublishing effort. You get a > 'Handle' (which is an alternative system to DOIs), making your figure > citable... E.g. > http://figshare.com/figures/index.php/DIC_microscopy_of_kinesin_aggregation > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Institutet för miljömedicin > Karolinska Institutet > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > ------------------------------------------------------------------------------ > 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 > ------------------------------------------------------------------------------ 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
