> To put one of the problems another way, the big problem is that, ultimately, > one would like a hieararchy with a molecule (protein) containing multiple > chains. The PDB reader can't, in general, create such a thing since it > doesn't know how the chains are grouped into molecules. As a result, it has > to return something intermediate. Currently it returns a hierarchy would > would have to be broken apart and put back tother in order to get the > presumably desired result. I would suggest producing a vector of molecules > instead so that the user can filter them/assemble them as needed. We could > provide special versions of the reader to handle easy cases (like where you > know the pdb file only contains one protein).
How about more simple solution: producing a vector of atoms (very well defined!) And the user can do with that what he wants later, build hierarchies, assemblies or whatever...