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). Before the recent rewrite, we stored clockwise/anticlockwise as an atom property (which led to various problems).
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. - Noel On 26 April 2010 08:59, Egon Willighagen <egon.willigha...@gmail.com> wrote: > Hi all, > > is anyone using IAtomParity in their software? If so, please let me > know as soon as possible, as I am working on a patch in this area and > need to decide on: > > 1. replace it with something CLOCKWISE, ANTI_CLOCKWISE, as used by e.g. SMILES > 2. generalize the stereochemistry framework to support both > > IAtomParity is based on 3D coordinates, resulting in a unique -1 or 1 > value, reflecting the absolute 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 > ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
