Ontologist, sigh. ChEBI also has subatomic particles :-). I agree with Nico in some respects and it makes sense if you have a database and ontologies. However these more complex abstracts are difficult to model efficiently. You need something specialised like OWL or Prolog but that's only useful for logic and not general computation.
It's much better to do one thing really well then to do many things poorly. The CDK is really slow and introducing a more complex object model will only make things worse. It's nice to try and satisfy all domains but in the end you need to have something which is actually useful. J On 7 Oct 2013, at 08:28, Egon Willighagen <[email protected]> wrote: > On Fri, Oct 4, 2013 at 4:32 PM, John May <[email protected]> wrote: >> There is no more Molecule in new CDK versions only AtomContainer, this could >> be confusing - vote here: http://strawpoll.me/501772 > > Nico Adams suggested on Google+ the obvious thing that I should have > thought of last Friday too... why not go semantic all the way, and use > ChemicalEntity as root container... > > I think this is the right (tm) solution. Seriously, why not take a > proven language like ChEBI, why not align with what the community has > come up as term for what it really is... > > 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 > > ------------------------------------------------------------------------------ > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk > _______________________________________________ > Cdk-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-devel ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
