Hi all, Klas seems to have problems with Indoles (and derivatives) :-)
c1ccc(C[C@@H](C(N[C@H](Cc2c3ccccc3[nH]c2)C(N[C@@H](CCCN)C(N[C@@H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H] Cl.Cl.Oc1ccc2CC3[C@](Cc4c(-c5ccccc5)c(C)[nH0](Cc5ccccc5)c4[C@@H]([C@](CCN3CC3CC3)(c2c1O1)2)1)2(O) Those are from my collection of CDK SDG layout nightmares :-) Kind regards, Chris -- Dr. Christoph Steinbeck Head of Cheminformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. On 14 May 2012, at 10:15, Egon Willighagen wrote: > Dear CDK and Bioclipse users, > > with this email I would like to ask 2 minutes of your time (no, I'm > not going to offer 1M euro via Mr. Williams :). One of the standing > issues in the CDK was the lack of a general-purpose implementation of > an algorithm to find the location of double bonds in delocalized > systems. Typical input where such localization information is missing > is SMILES and MDL molfiles that use the query bond order type 4 for > delocalized bond systems. > > The CDK had two main algorithms up to CDK 1.4.9: the SaturationChecker > and the DeduceBondSystemTool. But both had know situations where they > did not work well, and independently from each other two teams set up > to work on improving the situation. > > Kevin Lawson started from the direction of the DeduceBondSystemTool, > first focusing on speeding up the algorithm, later on other rewrites. > Klas Jönsson and me from the direction of the SaturationChecker, > improving it by having it use atom type knowledge. Patches for both > approaches are reaching a finalization phase, and while we already > tested our own tricky chemical structures, we seek your input. Please > follow these steps: > > 1. open the webpage Nina Jeliazkova has set up: > http://ambit.uni-plovdiv.bg:8080/dbst/depict/cdk > 2. enter your favorite SMILES with lower case organic subset elements, > e.g. c1ccccc1. > 3. check the double bond locations of these three algorithms: > - left is the old faithful DeduceBondSystemTool > - middle is Klas' AtomTypeAwareSaturationChecker > - right is Kevin's FixBondOrdersTool > 4. if Klas' and Kevin's do not find the right location of the double > bonds, please reply that SMILES to this email (or in your blog) > 5. optionally, report how many SMILES it did work properly for > > Your input on this is very much appreciated! > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > 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 > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Bioclipse-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/bioclipse-devel ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
