Merge pull request #6071 from RosettaCommons/vmullig/update_rms_functions Add some RMSD functions. This pull request: - [x] Adds a `superimpose_polymer_heavyatoms()` function, to superimpose based on either _all_ heavyatoms or all _mainchain_ heavyatoms. Our existing functions are peptide and protein-specific. - [x] Adds a `all_atom_rmsd_incl_hydrogens()` function (as well as a Doxygen comment on the existing `all_atom_rmsd()` function indicating that this excludes hydrogens). - [x] Switches a couple of instances of `new` to use `make_shared` instead. - [x] Unit tests this. These new functions are used in a project that will be the subject of a future pull request.