refactor: restructure dice environment handling and update Python version requirement

diceplayer/environment/molecule.py

@@ -2,7 +2,6 @@ from __future__ import annotations
 
 from diceplayer.environment import Atom
 from diceplayer.logger import logger
-from diceplayer.utils.cache import invalidate_computed_properties
 from diceplayer.utils.misc import BOHR2ANG, EA_2_DEBYE
 from diceplayer.utils.ptable import GHOST_NUMBER
 
@@ -15,7 +14,6 @@ from typing_extensions import List, Self, Tuple
 import math
 from copy import deepcopy
 from dataclasses import field
-from functools import cached_property
 
 
 @dataclass
@@ -34,11 +32,11 @@ class Molecule:
     molname: str
     atom: List[Atom] = field(default_factory=list)
 
-    @cached_property
+    @property
     def total_mass(self) -> float:
         return sum(atom.mass for atom in self.atom)
 
-    @cached_property
+    @property
     def com(self) -> npt.NDArray[np.float64]:
         com = np.zeros(3)
 
@@ -49,7 +47,7 @@ class Molecule:
 
         return com
 
-    @cached_property
+    @property
     def inertia_tensor(self) -> npt.NDArray[np.float64]:
         """
         Calculates the inertia tensor of the molecule.
@@ -79,7 +77,6 @@ class Molecule:
 
         return inertia_tensor
 
-    @invalidate_computed_properties()
     def add_atom(self, a: Atom) -> None:
         """
         Adds Atom instance to the molecule.
@@ -90,7 +87,6 @@ class Molecule:
 
         self.atom.append(a)
 
-    @invalidate_computed_properties()
     def remove_atom(self, a: Atom) -> None:
         """
         Removes Atom instance from the molecule.
@@ -101,7 +97,6 @@ class Molecule:
 
         self.atom.remove(a)
 
-    @invalidate_computed_properties()
     def move_center_of_mass_to_origin(self) -> None:
         """
         Updated positions based on the center of mass of the molecule
@@ -111,7 +106,6 @@ class Molecule:
             atom.ry -= self.com[1]
             atom.rz -= self.com[2]
 
-    @invalidate_computed_properties()
     def rotate_to_standard_orientation(self) -> None:
         """
         Rotates the molecule to the standard orientation
@@ -315,3 +309,12 @@ class Molecule:
         diff = coords_a[:, None, :] - coords_b[None, :, :]
         d2 = np.sum(diff**2, axis=-1)
         return np.sqrt(d2.min())
+
+    def signature(self) -> List[int]:
+        """
+        Returns the signature of the molecule, which is a list of the number of atoms of each type in the molecule.
+
+        Returns:
+            List[int]: signature of the molecule
+        """
+        return [a.lbl for a in self.atom]