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- Remove redundant or outdated code, improve typing and error handling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

@@ -1,4 +1,4 @@
-from diceplayer.utils.ptable import PTable
+from diceplayer.utils.ptable import PTable, AtomInfo
 
 from dataclasses import dataclass
 
@@ -21,3 +21,7 @@ class Atom:
     @property
     def mass(self) -> float:
         return PTable.get_atomic_mass(self.na)
+
+    @property
+    def atom_info(self) -> AtomInfo:
+        return PTable.get_from_atomic_number(self.na)