Refactor reaction mapping and duplicate handling for #25

.vscode/settings.json

@@ -1,5 +1,4 @@
 {
-    "python-envs.defaultEnvManager": "ms-python.python:system",
-    "python-envs.defaultPackageManager": "ms-python.python:pip",
-    "python-envs.pythonProjects": []
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda"
 }

AutoREACTER/detectors/functional_groups_detector.py

@@ -139,7 +139,7 @@ class MonomerEntry:
 # TODO: Add more functional groups as needed from literature/user requirements.
 
 
-@dataclass(slots=True, frozen=True)
+@dataclass(slots=True)
 class FunctionalGroupInfo:
     """
     Immutable dataclass storing information about a detected functional group.

AutoREACTER/detectors/reaction_detector.py

@@ -58,20 +58,8 @@ class EmptyReactionListError(Exception):
     This should be prevented by the reaction_selection method, but this error serves as a safeguard."""
     pass
 
-@dataclass(slots=True, frozen=True)
-class ReactionTemplate:
-    """
-    Defines a generic template for a polymerization reaction.
-    """
-    reaction_name: str
-    reactant_1: str                 # functional group name
-    reactant_2: Optional[str]       # functional group name or None
-    reaction_smarts: str
-    same_reactants: bool
-    delete_atom: bool
-    references: dict
 
-@dataclass(slots=True, frozen=True)
+@dataclass(slots=True)
 class ReactionInstance:
     """
     Represents a specific instance of a reaction between identified monomers.
@@ -90,6 +78,7 @@ class ReactionInstance:
     reaction_smarts: str
     delete_atom: bool
     references: dict
+    same_reactants: bool
     monomer_1: MonomerRole
     functional_group_1: FunctionalGroupInfo
     monomer_2: Optional[MonomerRole] = None
@@ -118,35 +107,27 @@ def _matching_fgs(self, monomer_entry: MonomerRole, target_group_name: str) -> L
         return [fg for fg in monomer_entry.functionalities if fg.fg_name == target_group_name]
 
     def _seen_pair_key(
-            self,
-            reaction_name: str,
-            monomer_role_1: MonomerRole,
-            fg_1: FunctionalGroupInfo,
-            monomer_role_2: Optional[MonomerRole] = None,
-            fg_2: Optional[FunctionalGroupInfo] = None,
-        ) -> Tuple:
-        """
-        Generates a unique, order-independent key for a reaction pair to avoid duplicates.
-
-        Args:
-            reaction_name: Name of the reaction.
-            monomer_role_1: First monomer.
-            fg_1: First functional group.
-            monomer_role_2: Second monomer (optional).
-            fg_2: Second functional group (optional).
-
-        Returns:
-            A tuple representing the unique state of this reaction instance.
-        """
+        self,
+        reaction_name: str,
+        monomer_role_1: MonomerRole,
+        fg_1: FunctionalGroupInfo,
+        monomer_role_2: Optional[MonomerRole] = None,
+        fg_2: Optional[FunctionalGroupInfo] = None,
+    ) -> Tuple:
+
         if monomer_role_2 is None or fg_2 is None:
-            return (reaction_name, monomer_role_1, fg_1)
+            return (
+                reaction_name,
+                monomer_role_1.smiles,
+                fg_1.fg_name
+            )
+
+        pair1 = (monomer_role_1.smiles, fg_1.fg_name)
+        pair2 = (monomer_role_2.smiles, fg_2.fg_name)
+
+        ordered = tuple(sorted([pair1, pair2]))
 
-        # Sort reactants by memory ID to ensure (A, B) and (B, A) produce the same key
-        ordered = tuple(sorted(
-            [(monomer_role_1, fg_1), (monomer_role_2, fg_2)],
-            key=lambda x: (id(x[0]), id(x[1]))
-        ))
-        return (reaction_name, ordered[0], ordered[1])
+        return (reaction_name, ordered)
 
     def reaction_detector(self, monomer_roles: List[MonomerRole]) -> List[ReactionInstance]:
         """
@@ -180,6 +161,7 @@ def reaction_detector(self, monomer_roles: List[MonomerRole]) -> List[ReactionIn
                                     reaction_smarts=reaction_info["reaction"],
                                     delete_atom=reaction_info["delete_atom"],
                                     references=reaction_info["reference"],
+                                    same_reactants=same_reactants,
                                     monomer_1=monomer_role,
                                     functional_group_1=fg
                                 )
@@ -210,6 +192,7 @@ def reaction_detector(self, monomer_roles: List[MonomerRole]) -> List[ReactionIn
                                             reaction_smarts=reaction_info["reaction"],
                                             delete_atom=reaction_info["delete_atom"],
                                             references=reaction_info["reference"],
+                                            same_reactants=same_reactants,
                                             monomer_1=monomer_role_i,
                                             functional_group_1=fg_i,
                                             monomer_2=monomer_role_j,
@@ -243,6 +226,7 @@ def reaction_detector(self, monomer_roles: List[MonomerRole]) -> List[ReactionIn
                                         reaction_smarts=reaction_info["reaction"],
                                         delete_atom=reaction_info["delete_atom"],
                                         references=reaction_info["reference"],
+                                        same_reactants=same_reactants,
                                         monomer_1=monomer_role,
                                         functional_group_1=fg_1,
                                         monomer_2=monomer_role,

AutoREACTER/detectors/reactions_library.py

@@ -51,8 +51,8 @@ def __init__(self):
             },
             "Hydroxy Acid Halides Hydroxy Acid Halides Polycondensation(Polyesterification)": {
                 "same_reactants": False,
-                "reactant_1": "hydroxy_acid_halides_monomer",
-                "reactant_2": "hydroxy_acid_halides_monomer",
+                "reactant_1": "hydroxy_acid_halide",
+                "reactant_2": "hydroxy_acid_halide",
                 "product": "polyester_chain",
                 "delete_atom": True,
                 "reaction": "[O;!$(OC=*):1]-[H:3].[CX3:2](=[O:5])[Cl,Br,I:4]>>[OX2:1]-[CX3:2](=[O:5]).[Cl,Br,I:4]-[H:3]",
@@ -62,7 +62,7 @@ def __init__(self):
             },
             "Hydroxy Acid Halides Polycondensation(Polyesterification)": {
                 "same_reactants": True,
-                "reactant_1": "hydroxy_acid_halides_monomer",
+                "reactant_1": "hydroxy_acid_halide",
                 "product": "polyester_chain",
                 "delete_atom": True,
                 "reaction": "[O;!$(OC=*):1]-[H:3].[CX3:2](=[O:5])[Cl,Br,I:4]>>[OX2:1]-[CX3:2](=[O:5]).[Cl,Br,I:4]-[H:3]",