remove is_aromatic from ring's attributes

meeko/macrocycle.py

@@ -83,9 +83,7 @@ def collect_rings(self, setup):
             setup.rings.keys()
         ):  # ring_id are the atom indices in each ring
             size = len(ring_id)
-            if setup.rings[ring_id].is_aromatic:
-                rigid_rings.append(ring_id)
-            elif size < self._min_ring_size:
+            if size < self._min_ring_size:
                 rigid_rings.append(ring_id)
                 # do not add rings > _max_ring_size to rigid_rings
                 # because bonds in rigid rings will not be breakable

meeko/molsetup.py

@@ -48,7 +48,6 @@
 
 DEFAULT_BOND_ROTATABLE = False
 
-DEFAULT_RING_IS_AROMATIC = False
 DEFAULT_RING_CLOSURE_BONDS_REMOVED = []
 DEFAULT_RING_CLOSURE_PSEUDOS_BY_ATOM = defaultdict
 # endregion
@@ -346,7 +345,6 @@ def from_json(obj: dict):
 @dataclass
 class Ring:
     ring_id: tuple
-    is_aromatic: bool = DEFAULT_RING_IS_AROMATIC
 
     @staticmethod
     def from_json(obj: dict):
@@ -370,14 +368,13 @@ def from_json(obj: dict):
             return obj
 
         # Check that all the keys we expect are in the object dictionary as a safety measure
-        expected_json_keys = {"ring_id", "is_aromatic"}
+        expected_json_keys = {"ring_id"}
         if set(obj.keys()) != expected_json_keys:
             return obj
 
         # Constructs a Ring object from the provided keys.
         ring_id = string_to_tuple(obj["ring_id"], int)
-        is_aromatic = obj["is_aromatic"]
-        output_ring = Ring(ring_id, is_aromatic)
+        output_ring = Ring(ring_id)
         return output_ring
 
 
@@ -1965,8 +1962,6 @@ def perceive_rings(self, keep_chorded_rings: bool, keep_equivalent_rings: bool):
         rings = hjk_ring_detection.scan(keep_chorded_rings, keep_equivalent_rings)
         for ring_atom_indices in rings:
             ring_to_add = Ring(ring_atom_indices)
-            if self._is_ring_aromatic(ring_atom_indices):
-                ring_to_add.is_aromatic = True
             self.rings[ring_atom_indices] = ring_to_add
         return
 
@@ -2264,7 +2259,6 @@ def default(self, obj):
         if isinstance(obj, Ring):
             return {
                 "ring_id": tuple_to_string(obj.ring_id),
-                "is_aromatic": obj.is_aromatic,
             }
         return json.JSONEncoder.default(self, obj)
 

test/json_serialization_test.py

@@ -525,8 +525,6 @@ def check_ring_equality(decoded_obj: Ring, starting_obj: Ring):
     """
     assert isinstance(decoded_obj.ring_id, tuple)
     assert decoded_obj.ring_id == starting_obj.ring_id
-    assert isinstance(decoded_obj.is_aromatic, bool)
-    assert decoded_obj.is_aromatic == starting_obj.is_aromatic
     return