Hi Noel, On Mon, Apr 26, 2010 at 10:22 AM, Noel O'Boyle <baoille...@gmail.com> wrote: > Have you considered adopting the same classes used by OpenBabel for > stereochemistry? Tetrahedral stereo is associated with a molecule, not > an atom, and the object stores a "from" atomId, 3 reference atomIds, > and a direction (either Clockwise or AntiClockwise).
Yeah, I think that makes sense. I am also looking into the model used by InChI. > Before the recent > rewrite, we stored clockwise/anticlockwise as an atom property (which > led to various problems). Yeah, that is something the CDK does right already :) Actually, the IAtomParity is quite good, but uses 3D coordinaees, and the problem is that common formats like SMILES use a different data model :( > If you do go down this road, it would be a simple matter to adapt > OpenBabel's code for generating these classes from 3D coordinates, 2D > coordiantes, etc. Any pointers? Or should I dig up the details in the source code? BTW, does the OB stereo model also do axial and planar stereochemistry? Egon -- Post-doc @ Uppsala University Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
