Heavy atoms RMSD calculation in caprieval

[VGPReys]

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Closes #836, by adding a new parameter allatoms in caprieval module.
By setting it to true, rmsd computation will be made on all heavy atoms.

[mgiulini]

looks good, but tests should be stricter in my opinion, especially about the coordinate loading..did you use another software to compare the all atoms results to the ones given by caprieval?

[mgiulini]

everything looks good, nice improvement!