Not optimizing will result in a lousy conformer. The default should not generate poor bond lengths or angles. I’m less concerned about torsions.
-Dave > On Jun 14, 2018, at 5:20 PM, Geoffrey Hutchison <geoff.hutchi...@gmail.com> > wrote: > > 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! > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fsdm.link%2Fslashdot&data=01%7C01%7Cdkoes%40pitt.edu%7C61e0a3fbc74047e38bcc08d5d24d6aec%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=DntHfBE2L6yxdbh0rfYJU4mqio%2BRet8cxarI4ajzJsQ%3D&reserved=0 > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fopenbabel-devel&data=01%7C01%7Cdkoes%40pitt.edu%7C61e0a3fbc74047e38bcc08d5d24d6aec%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=6AWBd9tQcyNGZnLmE91OLuG%2B0ICAOwXR6N%2BCBeu2iNQ%3D&reserved=0 ------------------------------------------------------------------------------ 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
