On 27/03/2013 17:35, Geoffrey Hutchison wrote: >> Maybe a proposed simplification of the valence system >> http://forums.openbabel.org/ImplicitH-failures-td2990439.html >> should be looked at again. > > > Copy/paste from Chris's earlier message: >> A simpler and more obvious model for this purpose has essentially a >> single IMPVAL for each charge state of the molecule. (Only if you are >> interested in radicals or hydrogen on the higher valency states of >> second row elements do you need another rule for each higher valence.) >> There is no need for any skilful fine tuning. It is more maintainable >> and will be faster because not so many SMARTS patterns need to be >> matched. Up to now, It has worked for everything I've tried (although >> this not very extensive), except with test_formula, where the fault is >> in a couple of erroneous results in formularesults.txt, which at least >> shows the old model was error-prone and needs some more tweaking of >> phosphate structures. > > > I would be strongly in favor of implementing such a change now. Performance > testing has suggested that we perform way too many SMARTS matching when doing > typical things like parsing SDF or aromaticity detection. > > Chris, do you think your revised model can be integrated now? Based on my > schedule, I think a v2.4 release would be mid-summer. I would like to finish > my distance geometry implementation for coordinate generation and conformer > sampling and I think there would be plenty for a new release. > > It seems like Craig and Noel are strongly in support of this too.
I'll have a go at resurrecting this. I agree with Craig that the inner workings of OB are a bit of a hotch- potch, probably reflecting what several different people thought was "obvious". Bit I suspect making all the changes suggested would be a lot of (boring) work - this was why MolCore was proposed. Chris ------------------------------------------------------------------------------ Own the Future-Intel® Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
