From: Egon W. <e.w...@sc...> - 2007-04-15 06:48:10
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On Saturday 14 April 2007, Jiao, Dazhi wrote: > >> The only problem is when there is a recursive Smarts inside the > >> brackets. Then we not only have QueryAtom, but also QueryAtomContainer. > >> I don't see how to modify the SmartsAtom. So I think instead, when > >> parsing smarts, we need to build a QueryAtomContainer when there is > >> Recursive Smarts in the Brackets. When there is no Recursive Smarts, > >> return a SmartsAtom. > > > > This is probably right; however it seems that when you have a > > QueryAtomContainer as a node in the parse tree, we might hit problems > > with the UniversalIsomoprhismTester which considers atoms/bonds but not > > whole containers. > > This is bothering me as well. As I am getting myself more familiar with > the API, I am not sure if this is doable just using the > QueryAtomContainer for the RecursiveSmarts. Maybe we need a > SMARTSAtomContainer, which could contain the logical relationship. But I > am not sure due to my lack of understanding of how the query are > actually done. What do you think? OK, this would indeed be a problem. I do not feel that the UIT will be able to support this. Might you show some SMARTS examples that use such set up? Does anyone know if MQL also have such constructs? Egon -- e.w...@sc... Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 |