Hi Nick, On Fri, Nov 12, 2010 at 11:29 AM, Nick Vandewiele <nick.vandewi...@ugent.be> wrote: > When you parse a SMILES or an InChI String containing stereo-descriptors > into a CDK object like AtomContainer or Molecule (employing those parsers > like InChIToStructure, SmilesParser), where is the stereo-information stored > in the CDK object?
SMILES @ and @@ information is read into a ITetrahedralChirality, which extends IStereoElement. Double bond stereo chemistry is not read, currently. Use IAtomContainer.stereoElements() (in 1.3.x). InChI stereochemistry for tetrahedral atoms is read as IAtomParity, which also extends IStereoElement. Here too, double bond stereochemistry is not read yet. Both models should be interconvertable, but that patch has yet to be written, deprecating IAtomParity. > Or is this information lost until now? Some information will be lost... such as the double bond stereochemistry. We are extending the CDK with more extensive stereochemistry support, but do not have a dedicated developer around to work on that right now :( Interested coders can contact me at cdk-devel@ ... any work on double bond stereochemistry will be very much appreciated by me and many CDK users. Egon -- Dr E.L. Willighagen Postdoctoral Research Associate University of Cambridge 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 ------------------------------------------------------------------------------ What happens now with your Lotus Notes apps - do you make another costly upgrade, or settle for being marooned without product support? Time to move off Lotus Notes and onto the cloud with Force.com, apps are easier to build, use, and manage than apps on traditional platforms. Sign up for the Lotus Notes Migration Kit to learn more. http://p.sf.net/sfu/salesforce-d2d _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
