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...