Changes and new functions for the calculation of RMS values between conformers of a molecule

- Update of documentation and addition of an optional argument to AlignMolConformers() to store the RMS values between the first conformer and the other aligned conformers
- New function GetConformerRMS() to calculate the RMS between two conformers of a molecules
- New function GetConformerRMSMatrix() to calculate the RMS matrix between all conformers of a molecule
Going to accept the pull request, but there should certainly be tests for this.