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/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
