You don't have to use SMARTS -- you could program the atom types with a set of if/else clauses. Essentially all of MMFF94 atom typing is done this way in Open Babel. It's probably more tedious, though.
> Sorry, but my question remains as to how can element is assigned its atom > type based solely on bond connectivities. Molecular mechanics implementations like GAFF define a set of atom types determined by humans. So if you have the valence bond structure of a molecule (i.e., atomic numbers, bonded neighbors, and bond types = double, triple, etc.) you should have everything needed for GAFF. The only "other" things I see in the list of GAFF atom types are ring membership and aromaticity. You can, most definitely, assign these based on bond connectivities. So I guess my question is -- what more do you think one would need beyond atomic numbers and bond connectivities? In the organic chemist's view of the world, that's essentially everything. Thanks, -Geoff ------------------------------------------------------------------------------ Write once. Port to many. Get the SDK and tools to simplify cross-platform app development. Create new or port existing apps to sell to consumers worldwide. Explore the Intel AppUpSM program developer opportunity. appdeveloper.intel.com/join http://p.sf.net/sfu/intel-appdev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
