On 01/11/2011 02:27, Geoff Hutchison wrote: > > On Oct 11, 2010, at 4:18 PM, Chris Morley wrote: > >> 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'd like to re-visit this idea now that we have some flexibility in the > development trunk. I tried last-year's patch, and saw ~14% speedup when > computing 279,000 formulas from a SD file. (The improvement comes from > eliminating the hybridization assignment.) > > (It also has the side benefit that we can try out ideas for MolCore rules > while testing them against existing OB tests.) > > Thoughts?
I think we need a 2.3.2 release fairly soon. There are a number of bugs, some of which were new in 2.3.1 which we need to correct. Could we aim for the beginning of January? There needs to be a tag copy of 2.3.1 and then I guess we can use the 2-3-x branch for these corrections, some of which are already in trunk. Will you make the tag and do the merging? We can then use the trunk to try the new valence model and your success with it is encouraging. I could upload it, unless you want to, when you have done the merging. I realize that it is not essential to wait, but it avoids possible complications. Since the trunk would then be aimed at 2.4.0 I guess it then would be appropriate to add mods which destroy the binary compatibility? (In the fingerprint code particularly, when I get round to it.) Chris ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
