On Wed, Feb 27, 2008 at 3:10 PM, Andreas Schüller <[EMAIL PROTECTED]> wrote: > I had a look at the list and have some questions:
Thanx for your critical analysis! I appreciate that very much. > 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? Right... one neighbor too much. Fixed by Miguel in the reaction/ branch: http://cdk.svn.sourceforge.net/viewvc/*checkout*/cdk/branches/miguelrojasch/reaction/src/main/org/openscience/cdk/config/data/cdk_atomtypes.xml?revision=HEAD&content-type=text%2Fxml > 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). planar3 is actually a sp2 hybridization too; the difference is where the LP or unpaired electron is located. For planar3, pz is filled with the LP or the unpaired electron, while for sp2 it is filled with electrons involved in a pi bond. It would be better to have full markup of which orbitals are involved in the atom type, and which are filled with what, but the CDK does currently not support that, though I'm silently working on a rewrite... > 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? Yes. Note that atom types can even be differentiated beyond the atom type... e.g. there is a N.amide atom type, in addition to the N.planar3. The reason for this flexibility is to be compatible with other atom typing schemes, such as used in force fields. The design goal is to have simple one-to-one translation tables. Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- 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
