Hi Andreas, On Wednesday 19 July 2006 18:36, Andreas Schüller wrote: > I've got some general questions regarding the treatment of > stereochemistry in the CDK. Is there any general concept on how stereo > information is stored in CDK structures?
For 2D diagrams there's the CDKConstants you mention below, but which CDK does not consider true stereo descriptors, like IAtomParity. That's the kind of stereochemistry you find in a SMILES: one central atom, 4 neighbors, and a -1 or +1 (@ and @@ in SMILES, possibly the otherway around). Both are potentially interconvertable... > There are some CDKConstants related to stereo chemistry: > STEREO_BOND_UP, STEREO_BOND_DOWN, STEREO_ATOM_PARITY_PLUS, etc. (9 in > total). These are only meant for nice 2D graphical diagrams, and not necessarily related to 3D stereochemistry. > Also there is a class clalled AtomParity and an interface IAtomParity > and the Atom class has a method setStereoParity(int stereoParity). Good, you found it :) > Then there is the SmilesGenerator which is able to create SMILES > containing stereo information from the 3D coordinates of the atoms using > the class BondTools. I think the SMILES generator has a clever algorithm to deduce 3D atom parities from 2D wedge bond enriched diagrams. This might better be put into a separate class, so that it can be used independent from SMILES generation too. > If I was to write a SMILES parser able to read stereo information, how > would I store this information within CDK? IAtomParity. If you have a clever algorithm would could assign wedge bond constants to bond, based on the 2D coordinates and the IAtomParity, this would be great, but an area where it is easy to fail to do it properly. Check the upcoming IUPAC recommendation on the use of wedge bonds, somewhere on the IUPAC website. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
