Hi, I have made some changes in the code, a quick and dirty hack to focus on the substructure search using the SMSD.
The results of the test run are here http://chembioinfo.wordpress.com/2011/03/03/is-the-smsd-slow-while-performing-substructure-searches/ Kindly leave your thought and comments. Best regards Asad On 2 Mar 2011, at 12:02, cdk-user-requ...@lists.sourceforge.net wrote: > Send Cdk-user mailing list submissions to > cdk-user@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/cdk-user > or, via email, send a message with subject or body 'help' to > cdk-user-requ...@lists.sourceforge.net > > You can reach the person managing the list at > cdk-user-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Cdk-user digest..." > > > Today's Topics: > > 1. Re: Isomorhism and MolHandler: removeHydrogen flag issue/bug > (Thomas Strunz) > 2. Re: Cdk-user Digest, Vol 58, Issue 1 (Nina Jeliazkova) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 1 Mar 2011 15:32:06 +0100 > From: Thomas Strunz <beginn...@hotmail.de> > Subject: Re: [Cdk-user] Isomorhism and MolHandler: removeHydrogen flag > issue/bug > To: <gilleain.torra...@gmail.com>, <cdk-user@lists.sourceforge.net> > Message-ID: <dub103-w60ef5f0ec75e00261bf6e2ee...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > 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 f?r milj?medicin >>> 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > Message: 2 > Date: Tue, 1 Mar 2011 17:26:52 +0200 > From: Nina Jeliazkova <jeliazkova.n...@gmail.com> > Subject: Re: [Cdk-user] Cdk-user Digest, Vol 58, Issue 1 > To: Egon Willighagen <egon.willigha...@gmail.com> > Cc: cdk-user@lists.sourceforge.net, Syed Asad Rahman <a...@ebi.ac.uk> > Message-ID: > <aanlktim9rpgmrgnjpz1bnpyc2kkzrfhkokkebrvgk...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On 1 March 2011 12:51, Egon Willighagen <egon.willigha...@gmail.com> wrote: > >> Hej Asad, >> >> On Tue, Mar 1, 2011 at 11:43 AM, Syed Asad Rahman <a...@ebi.ac.uk> wrote: >>> Can I know which algorithm did you use in the SMSD for substructure >> search? >> > > Algorithm.SubStructure > > Here is an excerpt of the testing code > > boolean bondSensitive = true; > boolean removeHydrogen = true; > Isomorphism comparisonSMSD = new Isomorphism(Algorithm.SubStructure, > bondSensitive); > > comparisonSMSD.init(query,mol, removeHydrogen,true); > > > Regards, > Nina > >> >> Of course, the invitation for a CDK News paper or a FigShare >> contribution showing the performance differences of UIT versus SMSD >> (various algos) extends to you too! I think many potential SMSD users >> love to see how much faster SMSD is. >> >> Egon >> >> -- >> Dr E.L. Willighagen >> Postdoctoral Researcher >> Institutet f?r milj?medicin >> 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 >> > -------------- next part -------------- > An HTML attachment was scrubbed... > > ------------------------------ > > ------------------------------------------------------------------------------ > 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 > > > End of Cdk-user Digest, Vol 58, Issue 3 > *************************************** ------------------------------------------------------------------------------ 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
