MOPAssembler: calculate a score for the quality of the MOP

[pwvbutler]

The assembler could return a score that takes into account how well the CBUs fit the assembly model (e.g. by the RMSD between binding sites) and the degree of atom overlap. This score could allow identifying poorly assembled MOPs easily and/or optimising the assembled structures.

[pwvbutler]

I have written a function that calculates the RMSD between binding sites. I will push this to a new branch and test further before merging.