From aaa6011d6bf3a06f5aaeb373f20ec2e1f84257a7 Mon Sep 17 00:00:00 2001
From: Guillaume Bouvignies <guillaume.bouvignies@ens.psl.eu>
Date: Thu, 13 Jun 2024 21:59:17 +0200
Subject: [PATCH] Fitting errors in Chemex v2024.05.2 with MC and BS syntaxes
 (Error #2) (#245)

Fixes #244
---
 chemex/parameters/spin_system/atom.py  | 36 ++++++++++++++++++++++++
 chemex/parameters/spin_system/group.py | 39 +++++++++++++++++++++++++-
 2 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/chemex/parameters/spin_system/atom.py b/chemex/parameters/spin_system/atom.py
index 9649577c..e47da978 100644
--- a/chemex/parameters/spin_system/atom.py
+++ b/chemex/parameters/spin_system/atom.py
@@ -3,7 +3,9 @@
 from __future__ import annotations
 
 from collections.abc import Hashable
+from copy import deepcopy
 from dataclasses import dataclass, field
+from typing import Self
 
 from .constants import CORRECT_ATOM_NAME
 from .nucleus import Nucleus, str2nucleus
@@ -69,3 +71,37 @@ def __str__(self) -> str:
             str: The name of the atom.
         """
         return self.name
+
+    def __deepcopy__(self, memo: dict[int, Self]) -> Self:
+        """Creates a deep copy of the Atom instance.
+
+        Args:
+            memo (dict[int, Self]): A dictionary of memoized objects.
+
+        Returns:
+            Self: A deep copy of the Atom instance.
+        """
+        if id(self) in memo:
+            return memo[id(self)]
+
+        # Create a new instance of Atom without calling __init__
+        cls = self.__class__
+        new_atom = cls.__new__(cls)
+
+        # Copy all attributes to the new instance
+        new_atom.name = deepcopy(self.name, memo)
+        new_atom.nucleus = deepcopy(self.nucleus, memo)
+
+        # Copy search_keys excluding self
+        new_search_keys = deepcopy(
+            {key for key in self.search_keys if key is not self}, memo
+        )
+        new_atom.search_keys = new_search_keys
+
+        # Add the new_atom to its own search_keys set
+        new_atom.search_keys.add(new_atom)
+
+        # Memoize the new instance
+        memo[id(self)] = new_atom
+
+        return new_atom
diff --git a/chemex/parameters/spin_system/group.py b/chemex/parameters/spin_system/group.py
index e61a49fc..8c6630fc 100644
--- a/chemex/parameters/spin_system/group.py
+++ b/chemex/parameters/spin_system/group.py
@@ -1,8 +1,10 @@
 from __future__ import annotations
 
 from collections.abc import Hashable
+from copy import deepcopy
 from functools import cache, total_ordering
 from re import search
+from typing import Self
 
 from .constants import AAA_TO_A
 
@@ -113,7 +115,7 @@ def __hash__(self) -> int:
         Returns:
             int: The hash value of the group.
         """
-        return hash(self.name)
+        return hash((self.symbol, self.number, self.suffix))
 
     def __bool__(self) -> bool:
         """Boolean representation of the Group object.
@@ -130,3 +132,38 @@ def __str__(self) -> str:
             str: The full name of the group.
         """
         return self.name
+
+    def __deepcopy__(self, memo: dict[int, Self]) -> Self:
+        """Deep copy of the Group object.
+
+        Args:
+            memo (dict[int, object]): A dictionary for tracking copied objects.
+
+        Returns:
+            Group: A deep copy of the group.
+        """
+        if id(self) in memo:
+            return memo[id(self)]
+
+        # Create a new instance of Group without calling __init__
+        cls = self.__class__
+        new_group = cls.__new__(cls)
+
+        # Deep copy all attributes to the new instance
+        new_group.symbol = deepcopy(self.symbol, memo)
+        new_group.number = deepcopy(self.number, memo)
+        new_group.suffix = deepcopy(self.suffix, memo)
+
+        # Copy search_keys excluding self
+        new_search_keys = deepcopy(
+            {key for key in self.search_keys if key is not self}, memo
+        )
+        new_group.search_keys = new_search_keys
+
+        # Add the new_group to its own search_keys set
+        new_group.search_keys.add(new_group)
+
+        # Memoize the new instance
+        memo[id(self)] = new_group
+
+        return new_group