refactor: modernize System and Molecule classes with dataclasses and cleanup

- Convert System and Molecule classes to use @dataclass and field for defaults
- Remove unused imports and legacy code from system.py
- Move print_charges_and_dipole method from System to Player for better separation of concerns
- Minor formatting and import order improvements for consistency

diceplayer/environment/atom.py

@@ -1,4 +1,4 @@
-from diceplayer.utils.ptable import PTable, AtomInfo
+from diceplayer.utils.ptable import AtomInfo, PTable
 
 from dataclasses import dataclass
 

diceplayer/environment/molecule.py

@@ -1,8 +1,5 @@
 from __future__ import annotations
 
-from dataclasses import dataclass, Field
-from functools import cached_property
-
 from diceplayer import logger
 from diceplayer.environment import Atom
 from diceplayer.utils.cache import invalidate_computed_properties
@@ -12,10 +9,12 @@ from diceplayer.utils.ptable import GHOST_NUMBER
 import numpy as np
 import numpy.typing as npt
 from numpy.linalg import linalg
-from typing_extensions import List, Tuple, Self
+from typing_extensions import List, Self, Tuple
 
 import math
 from copy import deepcopy
+from dataclasses import dataclass, field
+from functools import cached_property
 
 
 @dataclass
@@ -30,8 +29,9 @@ class Molecule:
         com (npt.NDArray[np.float64]): The center of mass of the molecule
         inertia_tensor (npt.NDArray[np.float64]): The inertia tensor of the molecule
     """
+
     molname: str
-    atom: List[Atom] = Field(default_factory=list)
+    atom: List[Atom] = field(default_factory=list)
 
     @cached_property
     def total_mass(self) -> float:
@@ -301,12 +301,16 @@ class Molecule:
         Returns:
             float: minimum distance between the two molecules
         """
-        coords_a = np.array([(a.rx, a.ry, a.rz) for a in self.atom if a.na != GHOST_NUMBER])
+        coords_a = np.array(
-        coords_b = np.array([(a.rx, a.ry, a.rz) for a in molec.atom if a.na != GHOST_NUMBER])
+            [(a.rx, a.ry, a.rz) for a in self.atom if a.na != GHOST_NUMBER]
+        )
+        coords_b = np.array(
+            [(a.rx, a.ry, a.rz) for a in molec.atom if a.na != GHOST_NUMBER]
+        )
 
         if len(coords_a) == 0 or len(coords_b) == 0:
             raise ValueError("No real atoms to compare")
 
         diff = coords_a[:, None, :] - coords_b[None, :, :]
-        d2 = np.sum(diff ** 2, axis=-1)
+        d2 = np.sum(diff**2, axis=-1)
         return np.sqrt(d2.min())

diceplayer/environment/system.py

@@ -1,15 +1,11 @@
-from diceplayer import logger
 from diceplayer.environment.molecule import Molecule
-from diceplayer.utils.misc import BOHR2ANG
 
-import numpy as np
+from typing_extensions import List
-from numpy import linalg
-from typing_extensions import List, Tuple
 
-import math
+from dataclasses import dataclass, field
-from copy import deepcopy
 
 
+@dataclass
 class System:
     """
     System class declaration. This class is used throughout the DicePlayer program to represent the system containing the molecules.
@@ -19,12 +15,8 @@ class System:
         nmols (List[int]): List of number of molecules in the system
     """
 
-    def __init__(self) -> None:
+    nmols: List[int] = field(default_factory=list)
-        """
+    molecule: List[Molecule] = field(default_factory=list)
-        Initializes an empty system object that will be populated afterwards
-        """
-        self.nmols: List[int] = []
-        self.molecule: List[Molecule] = []
 
     def add_type(self, m: Molecule) -> None:
         """
@@ -36,123 +28,3 @@ class System:
         if not isinstance(m, Molecule):
             raise TypeError("Error: molecule is not a Molecule instance")
         self.molecule.append(m)
-
-    def update_molecule(self, position: np.ndarray) -> None:
-        """Updates the position of the molecule in the Output file
-
-        Args:
-            position (np.ndarray): numpy position vector
-        """
-
-        position_in_ang = (position * BOHR2ANG).tolist()
-        self.add_type(deepcopy(self.molecule[0]))
-
-        for atom in self.molecule[-1].atom:
-            atom.rx = position_in_ang.pop(0)
-            atom.ry = position_in_ang.pop(0)
-            atom.rz = position_in_ang.pop(0)
-
-        rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
-        self.molecule.pop(-1)
-
-        logger.info("Projected new conformation of reference molecule with RMSD fit")
-        logger.info(f"RMSD = {rmsd:>8.5f} Angstrom")
-
-    def rmsd_fit(self, p_index: int, r_index: int) -> Tuple[float, Molecule]:
-        projecting_mol = self.molecule[p_index]
-        reference_mol = self.molecule[r_index]
-
-        if len(projecting_mol.atom) != len(reference_mol.atom):
-            raise RuntimeError(
-                "Error in RMSD fit procedure: molecules have different number of atoms"
-            )
-        dim = len(projecting_mol.atom)
-
-        new_projecting_mol = deepcopy(projecting_mol)
-        new_reference_mol = deepcopy(reference_mol)
-
-        new_projecting_mol.move_center_of_mass_to_origin()
-        new_reference_mol.move_center_of_mass_to_origin()
-
-        x = []
-        y = []
-
-        for atom in new_projecting_mol.atom:
-            x.extend([atom.rx, atom.ry, atom.rz])
-
-        for atom in new_reference_mol.atom:
-            y.extend([atom.rx, atom.ry, atom.rz])
-
-        x = np.array(x).reshape(dim, 3)
-        y = np.array(y).reshape(dim, 3)
-
-        r = np.matmul(y.T, x)
-        rr = np.matmul(r.T, r)
-
-        try:
-            evals, evecs = linalg.eigh(rr)
-        except Exception as err:
-            raise RuntimeError(
-                "Error: diagonalization of RR matrix did not converge"
-            ) from err
-
-        a1 = evecs[:, 2].T
-        a2 = evecs[:, 1].T
-        a3 = np.cross(a1, a2)
-
-        A = np.array([a1[0], a1[1], a1[2], a2[0], a2[1], a2[2], a3[0], a3[1], a3[2]])
-        A = A.reshape(3, 3)
-
-        b1 = np.matmul(r, a1.T).T  # or np.dot(r, a1)
-        b1 /= linalg.norm(b1)
-        b2 = np.matmul(r, a2.T).T  # or np.dot(r, a2)
-        b2 /= linalg.norm(b2)
-        b3 = np.cross(b1, b2)
-
-        B = np.array([b1[0], b1[1], b1[2], b2[0], b2[1], b2[2], b3[0], b3[1], b3[2]])
-        B = B.reshape(3, 3).T
-
-        rot_matrix = np.matmul(B, A)
-        x = np.matmul(rot_matrix, x.T).T
-
-        rmsd = 0
-        for i in range(dim):
-            rmsd += (
-                (x[i, 0] - y[i, 0]) ** 2
-                + (x[i, 1] - y[i, 1]) ** 2
-                + (x[i, 2] - y[i, 2]) ** 2
-            )
-        rmsd = math.sqrt(rmsd / dim)
-
-        for i in range(dim):
-            new_projecting_mol.atom[i].rx = x[i, 0]
-            new_projecting_mol.atom[i].ry = x[i, 1]
-            new_projecting_mol.atom[i].rz = x[i, 2]
-
-        projected_mol = new_projecting_mol.translate(reference_mol.com)
-
-        return rmsd, projected_mol
-
-    def print_charges_and_dipole(self, cycle: int) -> None:
-        """
-        Print the charges and dipole of the molecule in the Output file
-
-        Args:
-            cycle (int): Number of the cycle
-            fh (TextIO): Output file
-        """
-
-        logger.info("Cycle # {}\n".format(cycle))
-        logger.info("Number of site: {}\n".format(len(self.molecule[0].atom)))
-
-        chargesAndDipole = self.molecule[0].charges_and_dipole()
-
-        logger.info(
-            "{:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
-                chargesAndDipole[0],
-                chargesAndDipole[1],
-                chargesAndDipole[2],
-                chargesAndDipole[3],
-                chargesAndDipole[4],
-            )
-        )

diceplayer/player.py

@@ -267,8 +267,6 @@ class Player:
             if "position" not in result:
                 raise RuntimeError("Optimization failed. No position found in result.")
 
-            self.system.update_molecule(result["position"])
-
         else:
             if "charges" not in result:
                 raise RuntimeError(
@@ -277,13 +275,37 @@ class Player:
 
             diff = self.system.molecule[0].update_charges(result["charges"])
 
-            self.system.print_charges_and_dipole(cycle)
+            self.print_charges_and_dipole(cycle)
             self.print_geoms(cycle)
 
             if diff < self.config.gaussian.chg_tol:
                 logger.info(f"Charges converged after {cycle} cycles.")
                 raise StopIteration()
 
+    def print_charges_and_dipole(self, cycle: int) -> None:
+        """
+        Print the charges and dipole of the molecule in the Output file
+
+        Args:
+            cycle (int): Number of the cycle
+            fh (TextIO): Output file
+        """
+
+        logger.info("Cycle # {}\n".format(cycle))
+        logger.info("Number of site: {}\n".format(len(self.system.molecule[0].atom)))
+
+        chargesAndDipole = self.system.molecule[0].charges_and_dipole()
+
+        logger.info(
+            "{:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
+                chargesAndDipole[0],
+                chargesAndDipole[1],
+                chargesAndDipole[2],
+                chargesAndDipole[3],
+                chargesAndDipole[4],
+            )
+        )
+
     def print_geoms(self, cycle: int):
         with open(self.config.geoms_file, "a") as file:
             file.write(f"Cycle # {cycle}\n")

tests/shared/environment/test_molecule.py

@@ -68,15 +68,10 @@ class TestMolecule(unittest.TestCase):
             Atom(lbl=1, na=1, rx=1.0, ry=1.0, rz=1.0, chg=1.0, eps=1.0, sig=1.0)
         )
 
-        expected = [
+        expected = [[0.0, 1.73205081], [1.73205081, 0.0]]
-            [0.0, 1.73205081],
-            [1.73205081, 0.0]
-        ]
         actual = mol.distances_between_atoms()
 
-        npt.assert_almost_equal(
+        npt.assert_almost_equal(expected, actual)
-            expected, actual
-        )
 
     def test_inertia_tensor(self):
         mol = Molecule("test")