Dear Özgür, On Tue, Jun 1, 2010 at 6:43 PM, Özgür Demir <ode...@chemie.fu-berlin.de> wrote: > My compounds have Nitrogens with 4 Bonds.
An uncharged nitrogen with four neighbours? What is the molecular structure? > Is there a workaround for this problem? No, there is not really a 'workaround'. Many cheminformatics algorithms need to know some basic properties of atoms and use atom types as model for that. The solution to this problem is to define the atom properties for the atom type you have in your molecule, that is currently returning null. Can you give me the InChI of the molecule? Then I can add the missing atom type. > By the way computing qsar descriptors without adding hydrogens > yields the same error for some descriptor classes. Yes, adding hydrogens is only one algorithm that needs to know these atom properties. The best thing you can do, is put a filter in place before your QSAR descriptor calculation, and have it only be done on molecules for which the CDK was able to detect atom types for all atoms. 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
