From: Egon W. <ego...@gm...> - 2013-10-07 09:52:39
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John, others, On Mon, Oct 7, 2013 at 11:31 AM, John May <joh...@gm...> wrote: > I'm actually okay with ChemicalEntity but as a more appropriate name for the > existing ChemObject (which AtomContainer already extends). Now there is a class we must reconsider... ChemObject exists because we decided to have some core properties and no one came up with a better idea; it's the Java approach, I guess. And a Map on each atom and bond is questionable at least... Similarly, we for long want to remove all those *FooSet classes and just List<IAtomContainer>, ummm... List<IMolecule>, ummm.... List<IChemicalEntity>... Rajarshi, now that you have some time, want to push some of your ideas in this area in the master? > I think 1.7+ we'll need a long think about the object hierarchy and tighten > up the definitions a bit. I have no problem representing the complexity of > chemistry Agreed. To me naming of classes is quite orthogonal to the hierarchy... we can simply one, while keeping the other more complex. (where the one is the hierarchy :) > but it shouldn't try to encode an ontology in the classes. We most certainly don't have to replicate a full ontology. I have also the insight that while we should have ontologies to encode isotope information, the running CDK should use a simpler format which is way much faster at loading and smaller in size, and created from the proper source. John, we have a lot to do. But please don't forget, speed never was a goal! Functionality was, and that is what is what made the CDK big. Now we introduce speed, but have to be careful not to loose functionality in the process. We *can* do both. (In fact, a paper a year or two ago showed that the CDK was not really that slow at all... and sometimes even faster than C/C++... the reference should be somewhere in my CiteULike library... still, we can be faster, and you have done amazing work here.) Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) 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 ORCID: 0000-0001-7542-0286 |