Hey Egon, I had a look at the list and have some questions:
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? 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? -Andreas Egon Willighagen wrote: > Hi all, > > for those who are using trunk/, and I am happy to hear that an > increasing number of people are courageous enough to give it a go, you > may find a list of all defined atom types at this URL: > > http://cdk.svn.sourceforge.net/viewvc/*checkout*/cdk/trunk/cdk/src/main/org/openscience/cdk/config/data/cdk_atomtypes.xml?revision=HEAD&content-type=text%2Fxml > > By setting the mime type in the URL, Firefox should pick up the > associated XSLT stylesheet and create nice HTML output for display. > > This list is work on progress, and many elements are currently not > listed at all. Additionally, you may notice many charged atom types > and radicals, which are important for partial charge, IP, reaction > mechanism, etc calculations. Thank to Miguel for guiding me with > those. > > Additions, bug reports etc, always most welcome. As well, as running > the CDKAtomTypeMatcher from trunk/ against your favorite molecule data > set... previous tests against PubChem were quite promosing... > > If you like to contribute atom types, please email to this list the > following information: > > - identifier > - element > - formal charge > - hybridization (sp2, sp3, ...) > - neighbours (aka coordination number) > - pi bonds (aka number of pi electrons > - lone pairs > > And, importantly, an example of the atom type in the wild, e.g. > MolBase, MaCiE, PubChem, ... please give a URL deep linking into that > database or, the database identifier. > > Egon > ------------------------------------------------------------------------- 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
