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- Remove redundant or outdated code, improve typing and error handling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/utils/misc.py

@@ -13,6 +13,8 @@ import time
 BOHR2ANG: Final[float] = 0.52917721092
 ANG2BOHR: Final[float] = 1 / BOHR2ANG
 
+EA_2_DEBYE = 1 / 0.20819434
+
 
 #######################################  functions  ######################################