> 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. Thoughts? -Geoff ------------------------------------------------------------------------------ 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
