> 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...