On 08/07/2009 12:02 PM, Daniel Russel wrote: > So where do we stand? The key question is what do we want AtomType to mean?
In molecular mechanics packages atom types are usually separated from the PDB atom names (they are defined in the forcefield). Multiple PDB atom name/residue name pairs can map to a single atom type.
To avoid confusing our users we should probably not refer to "PDB atom types" anywhere, because what you are calling an atom type is really an atom name.
I think types that are not globally unique is just asking for trouble long term, so my vote is for 2, where the unique type name is derived from one of the existing lists of unique atom types (e.g. CHARMM or Mol2). This is distinct from the name of the atom, however, so a given atom Particle would need both a type and a name to play nicely with both PDB and forcefields.
Ben