Merge pull request #77 from xiaoruiDong/resonance

Add a dedicated resonance module

rdmc/mol.py

@@ -334,7 +334,7 @@ def Copy(
         Returns:
             RDKitMol: a copied molecule
         """
-        new_mol = RDKitMol(Chem.RWMol(self._mol, quickCopy, confId=confId))
+        new_mol = RDKitMol(Chem.RWMol(self._mol, quickCopy, confId))
         copy_attrs = copy_attrs or []
         for attr in copy_attrs:
             setattr(new_mol, attr, copy.deepcopy(getattr(self, attr)))

rdmc/mol_compare.py

@@ -9,6 +9,8 @@
 
 from rdkit.Chem.rdMolDescriptors import CalcMolFormula
 
+from rdmc.resonance import generate_resonance_structures
+
 
 def get_resonance_structure_match(
     mol1_res: List["RDKitMol"],
@@ -121,9 +123,6 @@ def is_same_complex(
     Returns:
         bool: Whether the two complexes are the same.
     """
-    if resonance:
-        from rdmc.resonance import generate_radical_resonance_structures
-
     if not isinstance(complex1, (list, tuple)):
         complex1 = list(complex1.GetMolFrags(asMols=True))
     if not isinstance(complex2, (list, tuple)):
@@ -140,7 +139,7 @@ def is_same_complex(
 
     for mol1 in mol1s:
         mol1_res = (
-            generate_radical_resonance_structures(mol1[0], kekulize=True)
+            generate_resonance_structures(mol1[0])
             if resonance
             else [mol1[0]]
         )
@@ -153,7 +152,7 @@ def is_same_complex(
             mol2_res = mol2_res_dict.get(i)
             if mol2_res is None:
                 mol2_res = (
-                    generate_radical_resonance_structures(mol2[0], kekulize=True)
+                    generate_resonance_structures(mol2[0])
                     if resonance
                     else [mol2[0]]
                 )

rdmc/reaction.py

@@ -15,7 +15,7 @@
 
 from rdmc import RDKitMol
 from rdmc.mol_compare import is_same_complex, is_equivalent_reaction
-from rdmc.resonance import generate_radical_resonance_structures
+from rdmc.resonance import generate_resonance_structures
 from rdmc.ts import get_all_changing_bonds
 
 
@@ -339,7 +339,6 @@ def is_resonance_corrected(self) -> bool:
     def apply_resonance_correction(
         self,
         inplace: bool = True,
-        kekulize: bool = True,
     ) -> "Reaction":
         """
         Apply resonance correction to the reactant and product complexes.
@@ -350,14 +349,14 @@ def apply_resonance_correction(
             # TODO: when the reactant and product are changed
             return self
         try:
-            rcps = generate_radical_resonance_structures(
-                self.reactant_complex, kekulize=kekulize
+            rcps = generate_resonance_structures(
+                self.reactant_complex,
             )
         except BaseException:
             rcps = [self.reactant_complex]
         try:
-            pcps = generate_radical_resonance_structures(
-                self.product_complex, kekulize=kekulize
+            pcps = generate_resonance_structures(
+                self.product_complex,
             )
         except BaseException:
             pcps = [self.product_complex]

rdmc/resonance/__init__.py

@@ -1,4 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-from rdmc.resonance.resonance import generate_radical_resonance_structures
+from rdmc.resonance.base import generate_resonance_structures
+# Make sure resonance algorithms are registered
+import rdmc.resonance.rdkit
+import rdmc.resonance.rmg

rdmc/resonance/base.py

@@ -0,0 +1,94 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from rdmc.resonance.utils import is_equivalent_structure
+
+
+class ResonanceAlgoRegistry:
+    _registry = {}
+
+    @classmethod
+    def register(cls, name: str):
+        def decorator(some_class):
+            cls._registry[name] = some_class
+            return some_class
+
+        return decorator
+
+    @classmethod
+    def get(cls, name: str):
+        return cls._registry.get(name)
+
+
+def _merge_resonance_structures(
+    known_structs: list,
+    new_structs: list,
+    keep_isomorphic: bool = False,
+):
+    """
+    Merge resonance structures by removing duplicates.
+    This is only used in combining resonance structures from different backends.
+
+    Args:
+        known_structs (list): A list of known resonance structures. This list will be modified in place.
+        new_structs (list): A list of new resonance structures.
+    """
+    if len(new_structs) <= 1:
+        # The new algorithm failed or only return the original molecule
+        return
+
+    structs_to_add = []
+    # Each method has its own de-duplicate method
+    # so don't append to known structs until all checked
+    for new_struct in new_structs:
+        for known_struct in known_structs:
+            if is_equivalent_structure(
+                ref_mol=known_struct,
+                qry_mol=new_struct,
+                isomorphic_equivalent=not keep_isomorphic,
+            ):
+                break
+        else:
+            structs_to_add.append(new_struct)
+    known_structs.extend(structs_to_add)
+
+
+def generate_resonance_structures(
+    mol: "Chem.RWMol",
+    keep_isomorphic: bool = False,
+    copy: bool = True,
+    backend: str = "all",
+    **kwargs,
+):
+    """
+    Generate resonance structures for a molecule.
+    """
+    if backend == "all":
+        algos = list(ResonanceAlgoRegistry._registry.values())
+        known_structs = algos[0](
+            mol=mol,
+            keep_isomorphic=keep_isomorphic,
+            copy=copy,
+            **kwargs,
+        )
+        for algo in algos[1:]:
+            new_structs = algo(
+                mol=mol,
+                keep_isomorphic=keep_isomorphic,
+                copy=copy,
+                **kwargs,
+            )
+            _merge_resonance_structures(known_structs, new_structs)
+
+        return known_structs
+
+    algo = ResonanceAlgoRegistry.get(backend)
+    if algo:
+        return algo(
+            mol=mol,
+            keep_isomorphic=keep_isomorphic,
+            copy=copy,
+            **kwargs,
+        )
+    else:
+        raise ValueError(f"Invalid backend {backend}")