Hi Gilleain, It would be good to have an option that just takes the atomcontainers as given or put the responsibility on the user of cdk.
Anway UIT seems much easier to handle and is in my cases not really slower than smsd but I work with small molecules. Another issue with smsd is, that in my application, it crashes when having 2 threads doing graph matching. With 2 threads running UIT, no problem. And it involves nothing else than changing about 3 lines of code. A mystery to me. Regards, Thomas > Date: Tue, 1 Mar 2011 11:41:49 +0000 > From: gilleain.torra...@gmail.com > To: cdk-user@lists.sourceforge.net > Subject: Re: [Cdk-user] Isomorhism and MolHandler: removeHydrogen flag > issue/bug > > 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
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