Bonds cannot be found for alternative atom names

[padix-key]

Following up #668, chem_comp_atom.alt_atom_id is part of the internal CCD, but is not used to determine bonds yet. However some (especially older) PDB entries contain those alternative atom names. For these connect_via_residue_names() cannot determine bonds, yet.

A solution would be mapping alternative atom names to their canonical ones before assigning bonds.

[nscorley]

I can pick this up -- will try and open a PR within the next week