On Fri, Jun 6, 2008 at 9:46 AM, Nina Jeliazkova <[EMAIL PROTECTED]> wrote: > > The QSAR descriptor classes are just (or should be) just wrappers > > around actual functionality... if there is some property for which the > > given substructure is interesting to be colored, it should have been > > available as separate API anyway... > > IMHO, this approach can complicate the code. Suppose I am calculating a > descriptor, that relies on finding set fragments. As a result, I would like > not only the final (numerical) value, but also the set of fragments (atom > and bonds) that had been used in the calculation. The most elegant approach > will need nothing different than descriptor API;
The descriptor API just defines how to get to a data matrix with column names. > it will be rather awkward > to peek the internals of the descriptor calculation via separate calls. Actually, peeking at the internals is important! CDK is not an end product, it's a development library and an educational tool. We don't want black boxes. > > So, I don't think we should extend the QSAR descriptor API with such > > functionality. > > What about just introducing a class, that will implement DescriptorResult > interface, but will also provide the desired functionality (selected > atoms/bonds)? Thus descriptor API will not be extended at all, just the > descriptors where "selection" is relevant will return the relevant class. I'm against this idea; I really think we should split algorithms from descriptors... what you are really interested in, is the outcome of some algorithm, not so much the calculated values. The descriptor API is about the latter, our convenience black box approach, which is why the should only be wrapping. The algorithm, instead, should allow peaking at details, such as which *bla* has been used to get to the numeric outcome. IMO Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
