From c563bf97bcff76bd0cdf451c50a2e29eaa7d4d92 Mon Sep 17 00:00:00 2001
From: diogom <diogom@scripps.edu>
Date: Sat, 11 Jan 2025 18:42:57 -0800
Subject: [PATCH] rename Bond's cycle_break to breakable

---
 meeko/molsetup.py               | 12 ++++++------
 meeko/preparation.py            |  2 +-
 test/json_serialization_test.py | 15 +++++++++++++++
 test/macrocycle_test.py         | 12 ++++++------
 4 files changed, 28 insertions(+), 13 deletions(-)

diff --git a/meeko/molsetup.py b/meeko/molsetup.py
index 88824ab6..5c67fb49 100644
--- a/meeko/molsetup.py
+++ b/meeko/molsetup.py
@@ -51,7 +51,7 @@
 DEFAULT_GRAPH = []
 
 DEFAULT_BOND_ROTATABLE = False
-DEFAULT_BOND_CYCLE_BREAK = False
+DEFAULT_BOND_BREAKABLE = False
 
 DEFAULT_RING_CLOSURE_BONDS_REMOVED = []
 DEFAULT_RING_CLOSURE_PSEUDOS_BY_ATOM = defaultdict
@@ -279,7 +279,7 @@ class Bond(BaseJSONParsable):
     index1: int
     index2: int
     rotatable: bool = DEFAULT_BOND_ROTATABLE
-    cycle_break: bool = DEFAULT_BOND_CYCLE_BREAK
+    breakable: bool = DEFAULT_BOND_BREAKABLE
 
     def __post_init__(self):
         self.canon_id = self.get_bond_id(self.index1, self.index2)
@@ -293,12 +293,12 @@ def json_encoder(cls, obj: "Bond") -> Optional[dict[str, Any]]:
                 "index1": obj.index1,
                 "index2": obj.index2,
                 "rotatable": obj.rotatable,
-                "cycle_break": obj.cycle_break,
+                "breakable": obj.breakable,
         }
         return output_dict
     
     # Keys to check for deserialized JSON 
-    expected_json_keys = {"canon_id", "index1", "index2", "rotatable", "cycle_break"}
+    expected_json_keys = {"canon_id", "index1", "index2", "rotatable"}
 
     @classmethod
     def _decode_object(cls, obj: dict[str, Any]): 
@@ -307,8 +307,8 @@ def _decode_object(cls, obj: dict[str, Any]):
         index1 = obj["index1"]
         index2 = obj["index2"]
         rotatable = obj["rotatable"]
-        cycle_break = obj["cycle_break"]
-        output_bond = cls(index1, index2, rotatable, cycle_break)
+        breakable = obj.get("breakable", DEFAULT_BOND_BREAKABLE)
+        output_bond = cls(index1, index2, rotatable, breakable)
         return output_bond
     # endregion
 
diff --git a/meeko/preparation.py b/meeko/preparation.py
index 1b5100bf..2f4cbcf4 100644
--- a/meeko/preparation.py
+++ b/meeko/preparation.py
@@ -336,7 +336,7 @@ def calc_flex(
 
         for atom1, atom2 in bonds_to_break:
             bond_id = Bond.get_bond_id(atom1, atom2)
-            setup.bond_info[bond_id].cycle_break = True
+            setup.bond_info[bond_id].breakable = True
 
         return
 
diff --git a/test/json_serialization_test.py b/test/json_serialization_test.py
index e153d1cb..b2b3627c 100644
--- a/test/json_serialization_test.py
+++ b/test/json_serialization_test.py
@@ -341,6 +341,21 @@ def test_dihedral_equality():
     check_molsetup_equality(starting_molsetup, decoded_molsetup)
     return
 
+
+def test_broken_bond(): 
+    fn = str(pkgdir / "test" / "macrocycle_data" / "lorlatinib.mol")
+    mol = Chem.MolFromMolFile(fn, removeHs=False)
+    mk_prep_untyped = MoleculePreparation(untyped_macrocycles=True)
+    starting_molsetup = mk_prep_untyped(mol)[0]
+    decoded_molsetup = RDKitMoleculeSetup.from_json(starting_molsetup.to_json())
+    count_rotatable = 0
+    count_breakable = 0
+    for bond_id, bond_info in decoded_molsetup.bond_info.items():
+        count_rotatable += bond_info.rotatable
+        count_breakable += bond_info.breakable
+    assert count_rotatable == 10
+    assert count_breakable == 1
+
 # endregion
 
 
diff --git a/test/macrocycle_test.py b/test/macrocycle_test.py
index f1556fe5..28f02512 100644
--- a/test/macrocycle_test.py
+++ b/test/macrocycle_test.py
@@ -109,19 +109,19 @@ def test_untyped_macrocycle():
     mk_prep_typed = MoleculePreparation()
     molsetup_typed = mk_prep_typed(mol)[0]
     count_rotatable = 0
-    count_broken = 0
+    count_breakable = 0
     for bond_id, bond_info in molsetup_typed.bond_info.items():
         count_rotatable += bond_info.rotatable
-        count_broken += bond_info.cycle_break
+        count_breakable += bond_info.breakable
     assert count_rotatable == 2
-    assert count_broken == 0
+    assert count_breakable == 0
 
     mk_prep_untyped = MoleculePreparation(untyped_macrocycles=True)
     molsetup_untyped = mk_prep_untyped(mol)[0]
     count_rotatable = 0
-    count_broken = 0
+    count_breakable = 0
     for bond_id, bond_info in molsetup_untyped.bond_info.items():
         count_rotatable += bond_info.rotatable
-        count_broken += bond_info.cycle_break
+        count_breakable += bond_info.breakable
     assert count_rotatable == 10
-    assert count_broken == 1
+    assert count_breakable == 1