Fixed an issue in the mmCIF reader for files starting with a ligand only chain. Before the first atom was stored in its own residue and the remaining atoms in a second residue. Happend for PDB entry 1AGA.

Ensures compilation in GCC compilers which have C++11 by default.

This function assumes the user knows what he's doing, this is also clearly
stated in the documentation:
"RMSD of atom positions (taken blindly in the order in
which the atoms appear) in the two given views."
This check at least avoids a segfault when the number of atoms does not
match. The result would be completely wrong anyway...

Hetatms are potentially skipped but if they come with an ANISOU record,
ost expects them to be there. As a solution we simply increase the
permissiveness as we already do it when having the calpha_only option
active.

* Added actions interface including one action to compare structures (meant to
  replace use of molck/lddt-binaries and make QS-scoring accessible)
* Added single chain lDDT scores using QS chain mapping and weighted average
* Added penalties for extra chains (ref and mdl) for oligo lDDT scores