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- Remove redundant or outdated code, improve typing and error handling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

@@ -0,0 +1,29 @@
+from functools import cached_property
+
+
+def invalidate_computed_properties():
+    """
+    Decorator function to invalidate the cached properties of the molecule when a new atom is added
+
+    Args:
+        properties (list[str]): list of the names of the properties to be invalidated
+    """
+
+    def get_cached_properies(cls: type) -> set[str]:
+        return {
+            name
+            for name, value in cls.__dict__.items()
+            if isinstance(value, cached_property)
+        }
+
+    def decorator(func):
+        def wrapper(self, *args, **kwargs):
+            result = func(self, *args, **kwargs)
+            for prop in get_cached_properies(self.__class__):
+                if hasattr(self, prop):
+                    delattr(self, prop)
+            return result
+
+        return wrapper
+
+    return decorator

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  ######################################