TST: Add first pass of tests for handling virtual sites in from_openmm

openff/interchange/_tests/conftest.py

@@ -13,21 +13,28 @@
 
 
 @pytest.fixture
-def sage():
+def sage() -> ForceField:
  return ForceField("openff-2.0.0.offxml")
 
 
 @pytest.fixture
-def sage_unconstrained():
+def sage_unconstrained() -> ForceField:
  return ForceField("openff_unconstrained-2.0.0.offxml")
 
 
 @pytest.fixture
-def sage_no_switch(sage):
+def sage_no_switch(sage) -> ForceField:
  sage["vdW"].switch_width = Quantity(0.0, "angstrom")
  return sage
 
 
+@pytest.fixture
+def sage_with_tip4p() -> ForceField:
+ # re-build off of existing fixtures if this gets implemented
+ # https:/openforcefield/openff-toolkit/issues/1948
+ return ForceField("openff-2.0.0.offxml", "tip4p.offxml")
+
+
 @pytest.fixture
 def sage_with_bond_charge(sage):
  sage["Bonds"].add_parameter(

openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py

@@ -12,9 +12,7 @@
 
 class TestUnsupportedCases:
  @pytest.mark.filterwarnings("ignore:.*are you sure you don't want to pass positions")
- def test_error_topology_mismatch(self, monkeypatch, sage_unconstrained, ethanol):
- monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
-
+ def test_error_topology_mismatch(self, sage_unconstrained, ethanol):
  topology = ethanol.to_topology()
  topology.box_vectors = Quantity([4, 4, 4], "nanometer")
 
@@ -38,23 +36,39 @@ def test_error_topology_mismatch(self, monkeypatch, sage_unconstrained, ethanol)
  topology=other_topology.to_openmm(),
  )
 
- def test_found_virtual_sites(self, monkeypatch, tip4p, water):
- monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
-
+ def test_found_out_of_plane_virtual_site(self, tip5p, water):
  topology = water.to_topology()
  topology.box_vectors = Quantity([4, 4, 4], "nanometer")
 
- system = tip4p.create_openmm_system(topology)
+ system = tip5p.create_openmm_system(topology)
 
  with pytest.raises(
  UnsupportedImportError,
- match="A particle is a virtual site, which is not yet supported.",
+ match="A particle is an `outOfPlane` virtual site, which is not yet supported.",
  ):
  from_openmm(
  system=system,
  topology=topology.to_openmm(),
  )
 
+ def test_found_two_particle_average_virtual_site(
+ self,
+ sage_with_bond_charge,
+ default_integrator,
+ ):
+ simulation = sage_with_bond_charge.create_interchange(
+ Molecule.from_smiles("CCl").to_topology(),
+ ).to_openmm_simulation(integrator=default_integrator)
+
+ with pytest.raises(
+ UnsupportedImportError,
+ match="A particle is a `TwoParticleAverage` virtual site, which is not yet supported.",
+ ):
+ from_openmm(
+ system=simulation.system,
+ topology=simulation.topology,
+ )
+
  def test_missing_positions_warning(self, monkeypatch, sage, water):
  monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
 

openff/interchange/_tests/unit_tests/interop/openmm/_import/test_virtual_sites.py

@@ -0,0 +1,56 @@
+import pytest
+from openff.toolkit import Topology
+
+from openff.interchange import Interchange
+from openff.interchange.components._packmol import solvate_topology
+from openff.interchange.drivers.openmm import _get_openmm_energies, get_openmm_energies
+
+
+class TestTIP4PVirtualSites:
+ def test_dimer_energy_equals(self, tip4p, water_dimer):
+ out: Interchange = tip4p.create_interchange(water_dimer)
+
+ roundtripped = Interchange.from_openmm(
+ system=out.to_openmm_system(),
+ topology=out.to_openmm_topology(collate=False),
+ positions=out.get_positions(include_virtual_sites=True).to_openmm(),
+ box_vectors=out.box.to_openmm(),
+ )
+
+ assert get_openmm_energies(out) == _get_openmm_energies(roundtripped)
+
+ def test_minimize_solvated_ligand(self, sage_with_tip4p, ethanol, default_integrator):
+ topology = solvate_topology(ethanol.to_topology())
+
+ simulation = sage_with_tip4p.create_simulation(
+ topology,
+ ).to_openmm_simulation(
+ integrator=default_integrator,
+ )
+
+ roundtripped = Interchange.from_openmm(
+ system=simulation.system,
+ topology=simulation.topology,
+ positions=simulation.context.getState(getPositions=True).getPositions(),
+ box_vectors=simulation.system.getDefaultPeriodicBoxVectors(),
+ )
+
+ original_energy = get_openmm_energies(simulation)
+
+ # TODO: Much more validation could be done here, but if a simulation
+ # can start and minimize at all, that should catch most problems
+ roundtripped.minimize()
+
+ assert get_openmm_energies(roundtripped) < original_energy
+
+ def test_error_index_mismatch(self, tip4p, water):
+ out: Interchange = tip4p.create_interchange(Topology.from_molecules([water, water]))
+
+ with pytest.raises(
+ ValueError, # TODO: Make a different error
+ match="The number of particles in the system and the number of atoms in the topology do not match.",
+ ):
+ Interchange.from_openmm(
+ system=out.to_openmm_system(),
+ topology=out.to_openmm_topology(collate=True),
+ )