refactor: modernize Molecule class with cached properties and vectorized operations

- Replace manual property updates with @cached_property for total_mass, com, and inertia_tensor
- Introduce invalidate_computed_properties decorator to auto-invalidate cached properties on atom changes
- Vectorize distances_between_atoms, sizes_of_molecule, and minimum_distance calculations using numpy
- Unify and clarify center of mass and standard orientation methods (move_center_of_mass_to_origin, rotate_to_standard_orientation)
- Remove redundant or outdated code, improve typing and error handling
- Update dependent files and tests to use new method names and behaviors

diceplayer/player.py

@@ -76,7 +76,7 @@ class Player:
                 "\n    Translating and rotating molecule to standard orientation..."
             )
 
-            mol.standard_orientation()
+            mol.rotate_to_standard_orientation()
             logger.info("\n Done")
             logger.info("\nNew values:\n")
             mol.print_mol_info()