[BUG] system.updateMolecules() doesn't work correctly for multiple molecules

[lohedges]

Currently the system.updateMolecules method doesn't work correctly when multiple molecules are passed in a list since the underlying Sire object (system._sire_object) is only udpated after the final molecule has been updated, not at each iteration. This breaks the logic since a copy of the system is used within the loop to avoid the original system being destroyed if Sire throws an exception on update.