Hi, > The atom types of "O.sp3" and "O.sp3.radical" look exactly the same. Is > the fact that one is a radical stored somehow as an atomic property? Not, It is not one has one ISingleElectron object and the other not. While O.sp3 explains the ether functional group, the O.sp3.radical is the result of the sigma-bond cleavage of an ether resulting an oxygen which contains one atom connected.
> Could you give an example for the "O.planar3" and "N.planar3" atom type? > I don't quite understand the geometry. Wait, the O in Furan could be > "O.planar3" and the N in Pyrrol is "N.planar3", right? If that's the > case, why is the hybridization of "O.planar3" set to "planar", instead > of "sp2" (my organics book claims that Furan's O is sp2). > Some atom types such as "O.sp3" and "O.planar3" are configured the same > (except for the hydridization type). Are they treated differently within > CDK? Right. The .planar3 and .sp2 represents the same geometry (planar )but for different atomtypes. Thus, O.planar3 is the ether functional group and O.sp2 represents the carbonyl group. Same geometry but different atomtype. Cheers, Miquel ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
