Enable PersesAtomMapper

openfe/setup/atom_mapping/perses_mapper.py

@@ -25,12 +25,36 @@
     allow_ring_breaking: bool
     preserve_chirality: bool
     use_positions: bool
+    coordinate_tolerance: unit.Quantity
+
+    def _to_dict(self) -> dict:
+        # strip units but record values
+        return {
+            "allow_ring_breaking": self.allow_ring_breaking,
+            "preserve_chirality": self.preserve_chirality,
+            "use_positions": self.use_positions,
+            "coordinate_tolerance": self.coordinate_tolerance.value_in_unit(
+                unit.angstrom
+            ),
+            "_tolerance_unit": "angstrom"
+        }
+
+    @classmethod
+    def _from_dict(cls, dct: dict):
+        # attach units again
+        tolerence_unit = dct.pop("_tolerance_unit")
+        dct["coordinate_tolerance"] *= getattr(unit, tolerence_unit)
+        return cls(**dct)
+
+    @classmethod
+    def _defaults(cls):
+        return {}
 
     @requires_package("perses")
     def __init__(self, allow_ring_breaking: bool = True,
                  preserve_chirality: bool = True,
                  use_positions: bool = True,
-                 coordinate_tolerance: float = 0.25 * unit.angstrom):
+                 coordinate_tolerance: unit.Quantity = 0.25 * unit.angstrom):
         """
         Suggest atom mappings with the Perses atom mapper.
 

openfe/tests/setup/atom_mapping/test_perses_atommapper.py

@@ -9,7 +9,6 @@
 USING_NEW_OFF = True  # by default we are now
 
 
-@pytest.mark.xfail(USING_NEW_OFF, reason="Perses #1108")
 def test_simple(atom_mapping_basic_test_files):
     # basic sanity check on the LigandAtomMapper
     mol1 = atom_mapping_basic_test_files['methylcyclohexane']
@@ -25,7 +24,6 @@
     assert len(mapping.componentA_to_componentB) == 4
 
 
-@pytest.mark.xfail(USING_NEW_OFF, reason="Perses #1108")
 def test_generator_length(atom_mapping_basic_test_files):
     # check that we get one mapping back from Lomap LigandAtomMapper then the
     # generator stops correctly
@@ -41,7 +39,6 @@
         next(mapping_gen)
 
 
-@pytest.mark.xfail(USING_NEW_OFF, reason="Perses #1108")
 def test_empty_atommappings(mol_pair_to_shock_perses_mapper):
     mol1, mol2 = mol_pair_to_shock_perses_mapper
     mapper = PersesAtomMapper()
@@ -53,3 +50,10 @@
 
     with pytest.raises(StopIteration):
         next(mapping_gen)
+
+
+def test_dict_round_trip():
+    # use some none defaults
+    mapper1 = PersesAtomMapper(allow_ring_breaking=False, preserve_chirality=False)
+    mapper2 = PersesAtomMapper.from_dict(mapper1.to_dict())
+    assert mapper2.to_dict() == mapper1.to_dict()