Hello CDK-people, To get the introduction out of the way: Hi, I'm Jules Kerssemakers, a recently started bioinformatics PhD student at the group of Gert Vriend (CMBI, netherlands). I work on the BioMeta database (http://biometa.cmbi.ru.nl) for metabolites and metabolism, which I took over from my predecessor, Martin Ott. Primary item on the agenda (before I start the actual science-y work) is an update of the information contained in the database (it's mostly based on the 2005 version of the KEGG database)
In an effort to automate this update procedure, I discovered the CDK. I can see it's a very powerful toolkit, but I'm having some trouble navigating the feature-set. To compare the molecules-to-update, I'm interested in the amount of defined/undefined stereocenters and defined/undefined double bond configurations. Does the CDK have a way to calculate these properties? I already found EgonW's blog about the CIPTool, (http://chem-bla-ics.blogspot.com/2010/04/cip-rules-for-stereochemistry.html), but I haven't been able to find it in CDK v1.2.5 nor in v1.3.5. I'm also unsure if the CIPtool would let me detect undefined stereocenters. So, summing up: -Can the CDK count defined/undefined stereocenters and/or double bonds, or do I need to do some (heavy) programming myself? Kind regards, Jules Kerssemakers ------------------------------------------------------------------------------ ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
