Hi Nick, On Wed, Aug 31, 2011 at 10:08 PM, Nick Vandewiele <nick.vandewi...@ugent.be> wrote: > However, adapting internal CDK code would > still be a major hurdle for many people that have absolutely no > programming background.
True. But that's what open collaborations are for... > Do you think it is feasible to automate the additions of newly defined atom > types in CDKAtomTypeMatcher? It seems to me that all the > “perceiveX(IAtomContainer, IAtom)” methods contains multiple nested > conditionals I'd say it is tricky... the problem is how to handle missing information, such comes from SMILES input and others... that is less obvious to automate... > checking the formal charge, etc. which could be automatically retrieved from > the owl dictionary, since every element in the owl dictionary contains all > of these attributes. True. Again, the missing information is not solved by this, but your point is fair. The current implementation should be seen as a reference implementation. But other approaches are not impossible... > I am probably overseeing some vital part in all of this… J Dunno. I think other approaches should be able to handle missing information too... the current implementation was just to get things going, and may not be the fastest approach. It's kind of a decision tree. Another tricky thing, is that some atom types depend on the perceived atom types in their neighborhood... e.g. N.planar3 versus N.sp2. Combine this with missing information, and you'll understand why atom types of nitrogens are hard to perceive correctly :) Thus, no, you're not missing anything. No one tried an alternative impl yet, though. The things I pointed out are only things to keep in mind; they're not points that make the current impl the only possible one, or best one, or special in any other way. Egon -- Dr E.L. Willighagen Postdoctoral Researcher Institutet för miljömedicin Karolinska Institutet (http://ki.se/imm) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
