Rajarshi has patched trunk last night with his work to address a few practical issues in the molecular descriptor module of the CDK (and I peer reviewed this work yesterday). One major change is that the IMolecularDescriptor calculate() method no longer throws an Exception, but returns Double.NaN instead. The Exception is stored in the DescriptorValue for convenience. This simplifies the QSAR descriptor calculation considerably, and, importantly, makes it more robust to the input. Though only by propagating errors into descriptor matrix. Just make sure your molecular structures have explicit hydrogens and 3D coordinates, and you’re fine.

Anyway, Rajarshi also added a new page to CDK Nightly to list the available descriptors:

This post was originally posted as https://chem-bla-ics.blogspot.com/2008/07/molecular-qsar-descriptors-in-cdk.html.