Note, however, my earlier point, so there is no room for confusion: multiple atoms in a given residue can have the same atom type (e.g. all the hydrogens may have the same type). The atom type does not suffice to uniquely define the atom name - that's why you need a separate atom name. And this would certainly need to be user- settable if the user wants to make any novel molecules that don't currently exist in the topology file/ligand database.I thought you said you could use the topology file to go from charmm atom types to pdb names? Or do you also need bonds or other non-type information? Which might be OK, but perhaps complicated.
If a user wants to name an atom, they can just name the particle, so that is well solved.The important distinction here is that atom names are just a construct to make humans' lives easier, while atom types are what the universe cares about.
The important thing is to have a minimal scheme for tagging atoms which supports something like
1) figure out which atoms are bonded to which other atoms 2) figure out how to set up a forcefield for the atoms 3) write a pdb file 4) write a mol2 file 5) allow one to figure out the element
Identifying atoms via their PDB names and the type of their parent as is currently sort of done, works fine.
So what is a minimal set of CHARMM-related information that can do what we need? Is it simpler/more useful than the PDB-based alternative?