Update of the System class

[ppravatto]

The System class, encoding a molecule, contains an attribute geometry of type MolecularGeometry that encodes the position and type of each atom. The computed properties are stored in the properties attribute of type Properties.

If geometry operations (translations, rotations, reflections, etc.) are implemented, their application may require the update or removal of already computed properties. In particular, as an example, every non-scalar property, such as normal modes, dipole moment, etc., must be updated if a rotation is applied to the molecular geometry.

We should discuss:

1. How should we implement these new features? Should we incorporate the MolecularGeometry class in the System class?
2. How should we handle the geometry operation? Should we apply the operations to the non scalar properties or should we clean the properties as if the geometry level of theory has been changed?
3. Do we accept the fact that some software may return slightly different results depending upon the orientation of the molecule (e.g. different orientation when defining the integration grid?) and as such the result obtained would not match exactly the transformed ones?