update perses atom mapper to use openff units

openfe/setup/atom_mapping/perses_mapper.py

@@ -6,8 +6,10 @@
 
 """
 
-from openmm import unit
 from openfe.utils import requires_package
+from openff.models.types import FloatQuantity
+from openff.units import unit
+from openff.units.openmm import to_openmm
 
 from ...utils.silence_root_logging import silence_root_logging
 try:
@@ -25,15 +27,15 @@ class PersesAtomMapper(LigandAtomMapper):
     allow_ring_breaking: bool
     preserve_chirality: bool
     use_positions: bool
-    coordinate_tolerance: unit.Quantity
+    coordinate_tolerance: FloatQuantity['angstrom']
 
     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(
+            "coordinate_tolerance": self.coordinate_tolerance.m_as(
                 unit.angstrom
             ),
             "_tolerance_unit": "angstrom"
@@ -67,7 +69,7 @@ def __init__(self, allow_ring_breaking: bool = True,
             if mappings must strictly preserve chirality, default: True
         use_positions: bool, optional
             this option defines, if the
-        coordinate_tolerance: openmm.unit.Quantity, optional
+        coordinate_tolerance: openff.units.unit.Quantity, optional
             tolerance on how close coordinates need to be, such they
             can be mapped, default: 0.25*unit.angstrom
 
@@ -81,7 +83,7 @@ def _mappings_generator(self, componentA, componentB):
         # Construct Perses Mapper
         _atom_mapper = AtomMapper(
             use_positions=self.use_positions,
-            coordinate_tolerance=self.coordinate_tolerance,
+            coordinate_tolerance=to_openmm(self.coordinate_tolerance),
             allow_ring_breaking=self.allow_ring_breaking)
 
         # Try generating a mapping

openfe/tests/setup/atom_mapping/test_perses_atommapper.py

@@ -2,6 +2,7 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import pytest
 from openfe.setup.atom_mapping import PersesAtomMapper, LigandAtomMapping
+from openff.units import unit
 
 pytest.importorskip('perses')
 pytest.importorskip('openeye')
@@ -54,6 +55,10 @@ def test_empty_atommappings(mol_pair_to_shock_perses_mapper):
 
 def test_dict_round_trip():
     # use some none defaults
-    mapper1 = PersesAtomMapper(allow_ring_breaking=False, preserve_chirality=False)
+    mapper1 = PersesAtomMapper(
+        allow_ring_breaking=False,
+        preserve_chirality=False,
+        coordinate_tolerance=0.01 * unit.nanometer
+    )
     mapper2 = PersesAtomMapper.from_dict(mapper1.to_dict())
     assert mapper2.to_dict() == mapper1.to_dict()