On Tue, Sep 29, 2009 at 11:24 PM, Craig A. James <cja...@emolecules.com> wrote: > Tim Vandermeersch wrote: >> >> On Tue, Sep 29, 2009 at 10:50 PM, Noel O'Boyle <baoille...@gmail.com> >> wrote: >>> >>> Nice work. >>> http://timvdm.blogspot.com/2009/09/automorphism-group-bliss.html >>> >>> Does this mean you've solved the problem? >> >> Yes, but to continue towards correct canonical codes, we still need to >> do some matrix math. The easiest solution would be to use Eigen 2 but >> I'm not sure trunk should already depend on it... I can use git(hub) >> for now. >> >> I think we should also remove the "break chiral ties" step. The new >> FindStereogenicUnits function finds these stereocenters now regardless >> of duplicated symmetry classes. This would mean symmetry classes are >> topologically only (not regarding stereochemistry). > > This is correct. The "break chiral ties" step is only there because the > initial symmetry analysis doesn't account for the chirality in the first > place. Reading your series of blogs, it's clear that incorporating > chirality into the symmetry analysis itself is a better algorithm. > > One question: it looks to me like the symmetry classes, and consequently the > canonical labels, will be completely different using this new method, which > means the canonical SMILES will all change. That's not a bad thing when > weighed against the improved algorithm, just something to consider.
Correct. That's why I'll be using github for a while untill I have something stable. I don't want to change trunk so it puts out different canonical smiles every day... ------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
