Merge pull request #178 from openforcefield/fix-177

Fix 177

openff/fragmenter/_tests/test_fragmenter.py

@@ -584,6 +584,16 @@ def test_add_substituent():
     assert fragment.to_smiles(mapped=False, explicit_hydrogens=False) == "CCCCCC"
 
 
+def test_issue_177():
+    """
+    There was an where the path search gets tripped up when there are two paths
+    of equal length leading to a 3-membered ring. This test ensures Fragmenter
+    runs on a minimal reproducing example of this problem.
+    More info at https://github.com/openforcefield/openff-fragmenter/issues/177
+    """
+    WBOFragmenter().fragment(Molecule.from_smiles("C1CC1[C@H]2C[C@H]3C[C@H]3C2"))
+
+
 @pytest.mark.parametrize("input_smiles, n_output", [("CCCCCCC", 4)])
 def test_pfizer_fragmenter(input_smiles, n_output):
     result = PfizerFragmenter().fragment(Molecule.from_smiles(input_smiles))

openff/fragmenter/fragment.py

@@ -1246,20 +1246,23 @@ def _select_neighbour_by_path_length(
 
         target_indices = [get_atom_index(molecule, atom) for atom in target_bond]
 
-        path_lengths_1, path_lengths_2 = zip(
-            *(
-                (
-                    networkx.shortest_path_length(
-                        nx_molecule, target_index, neighbour_index
+        path_lengths = list(
+            zip(
+                *(
+                    (
+                        networkx.shortest_path_length(
+                            nx_molecule, target_index, neighbour_index
+                        )
+                        for target_index in target_indices
                     )
-                    for target_index in target_indices
+                    for atom_index, neighbour_index in atoms_to_add
                 )
-                for atom_index, neighbour_index in atoms_to_add
             )
         )
 
-        if len(path_lengths_1) == 0 and len(path_lengths_2) == 0:
+        if len(path_lengths) == 0:
             return None
+        path_lengths_1, path_lengths_2 = path_lengths
 
         reverse = False