On 2013-04-26 21:22, Geoffrey Hutchison wrote: >> I assume it works like this that OB determines the atom type to be HO (H >> bound to O). > > No, no. This file is like a big translation dictionary. It says "if an atom > type comes in from a PCModel file with atom type X," that's equivalent to .. > well, everything on that row. Obviously, this need not be a one to one > mapping. HO is a particularly good example, since I think PCModel has the > "MMX" force field and separates between different types of HO hydrogens -- > sorry I can't find the MMX atom type list right now. > > So we could, in principal, have the internal atom types as a superset of all > atom types, but I think this is a bit crazy. > > If you want the internal atom typing rules, see data/atomtyp.txt > (particularly EXTTYP). > > Hope that helps, > -Geoff > Thanks for pointing that out. This means in practice that OB can not distinguish between all those atomtypes that are used in random packages, right?
It would still be useful to have a textual description of each OB atom type, what information there is in atomtyp.txt is not very descriptive. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with <2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
