Hi, One of the GSoC projects this summer is an improved fragment-based coordinate generation method. While that's going, I've been reading a lot of papers on 3D coordinate generation.
As near as I can tell, no other program attempts to do a conformer search as part of the 3D generation. Everyone just generates one 3D geometry and then lets people do conformer searching on top if they choose. Some of the papers (e.g. Pierre Baldi) compare to Open Babel and then say that babel is slow - but that's because a lot more work is performed. I'd like to change --gen3d to default to creating a geometry. Optionally, geometry optimization can be performed, but the conformer searching will be separate: --gen3d # default: will only create a geometry --gen3d=opt # will perform MMFF or UFF optimization on the geometry I think for many uses, this will provide much faster performance. Thoughts? Concerns? -Geoff ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
