On Thu, Jul 1, 2010 at 11:02 AM, Noel O'Boyle <baoille...@gmail.com> wrote: > On 30 June 2010 16:44, Geoffrey Hutchison <ge...@geoffhutchison.net> wrote: >>> bliss. bliss is GPLv2 and available from >>> http://www.tcs.hut.fi/Software/bliss/. My code also has a dependency >>> on Eigen2. >> >> I'm not thrilled at the idea of adding additional dependencies. I know >> people like Kabsch alignment, but we can also distribute a "contributed" >> program for those who want it and are willing to install bliss separately. > > Hmmm...well, the additional dependency could be circumvented if we had > an isomorphism tester (essentially, do these two sets of atoms map > onto each other?). This would not be as efficient as using bliss, but > it would work. I'll hold the code back (well, it's available on my > github mirror) then until we have one of these.
Writing an efficient automorphism algorithm is not trivial. Checking all permutations for equivalent symmetry classes is not acceptable for general use (I used it for validation in the past). Inositol could easily take several hours. I have not tried to make use of connectivity yet (like we do for substructure isomorphisms) but this might be enough to make performance acceptable. For inositol, there are 12 automorphisms. If the first of the 6 C atom is placed, there are two paths to close the ring resulting in 12 automorphisms. Bliss & nauty probably has many more of these optimizations. We could also provide an interface with multiple backends... (our own version, bliss, nauty) Tim >>> How about Eigen2? Should I just optionally compile? >> >> Eigen2 is already optionally detected if installed. Some of the charge >> models use it (namely QEq and QTPIE). >> >> Hope that helps, >> -Geoff >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> OpenBabel-Devel mailing list >> OpenBabel-Devel@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-devel >> > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by Sprint > What will you do first with EVO, the first 4G phone? > Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
