Merge branch 'main' into optional_filter_ordering

src/kartograf/filters/ring_changes.py

@@ -156,8 +156,9 @@ def get_atom_ring_hybridization_map(rdmol: Chem.Mol) -> dict[int, bool]:
     # Filtering Mapping
     filtered_mapping = {}
     for ai, aj in mapping.items():
-        ai_only_arom_sys = atomA_ring_hyb_map[ai]
-        aj_only_arom_sys = atomB_ring_hyb_map[aj]
+        # if the atom is not in a ring return False
+        ai_only_arom_sys = atomA_ring_hyb_map.get(ai, False)
+        aj_only_arom_sys = atomB_ring_hyb_map.get(aj, False)
 
         if ai_only_arom_sys == aj_only_arom_sys:
             filtered_mapping[ai] = aj

src/kartograf/tests/test_atom_mapper.py

@@ -6,7 +6,11 @@
 from kartograf.atom_mapper import (filter_atoms_h_only_h_mapped,
                                    filter_whole_rings_only)
 from kartograf.filters.element_change import filter_hybridization_changes
-from kartograf.filters.ring_changes import filter_whole_rings_only
+from kartograf.filters.ring_changes import (
+    filter_whole_rings_only,
+    filter_hybridization_rings,
+)
+
 
 from .conftest import (
     naphtalene_benzene_molecules,
@@ -312,3 +316,21 @@ def test_hybridization_and_ring_breaks(shp2_hybridization_ligands):
     )
     # make sure there was no change in the mapping
     assert filtered_mapping == mapping.componentA_to_componentB
+
+
+def test_ring_hybridization_with_non_ring_atoms(shp2_hybridization_ligands):
+    """
+    Make sure this filter does not fail on non-ring atoms see
+    <https://github.com/OpenFreeEnergy/kartograf/issues/62>
+    """
+    mapper = KartografAtomMapper(
+        additional_mapping_filter_functions=[filter_hybridization_rings]
+    )
+    mapping = next(
+        mapper.suggest_mappings(
+            shp2_hybridization_ligands[0],
+            shp2_hybridization_ligands[1]
+        )
+    )
+    # make sure we have some mapping between the atoms
+    assert mapping.componentA_to_componentB