Improve testing of GROMACS import

openff/interchange/_tests/__init__.py

@@ -76,9 +76,9 @@ class MoleculeWithConformer(Molecule):
     """Thin wrapper around `Molecule` to produce an instance with a conformer in one call."""
 
     @classmethod
-    def from_smiles(self, smiles, name="", **kwargs):
+    def from_smiles(self, smiles, name="", *args, **kwargs):
         """Create from smiles and generate a single conformer."""
-        molecule = super().from_smiles(smiles, **kwargs)
+        molecule = super().from_smiles(smiles, *args, **kwargs)
         molecule.generate_conformers(n_conformers=1)
         molecule.name = name
 

openff/interchange/_tests/_gromacs.py

@@ -3,14 +3,24 @@
 from openff.utilities import temporary_cd
 
 from openff.interchange import Interchange
+from openff.interchange.components.mdconfig import get_smirnoff_defaults
 from openff.interchange.drivers import get_gromacs_energies
 
 
-def gmx_monolithic_vs_itp(state: Interchange):
+def gmx_roundtrip(state: Interchange, apply_smirnoff_defaults: bool = False):
     with temporary_cd():
-        get_gromacs_energies(state, _monolithic=True).compare(get_gromacs_energies(state, _monolithic=False))
+        state.to_gromacs(prefix="state", decimal=8)
+        new_state = Interchange.from_gromacs(topology_file="state.top", gro_file="state.gro")
+
+        get_smirnoff_defaults(periodic=True).apply(new_state)
+
+        get_gromacs_energies(state).compare(get_gromacs_energies(new_state))
 
+
+def gmx_monolithic_vs_itp(state: Interchange):
+    with temporary_cd():
         # TODO: More helpful handling of failures, i.e.
         #         * Detect differences in positions
         #         * Detect differences in box vectors
         #         * Detect differences in non-bonded settings
+        get_gromacs_energies(state, _monolithic=True).compare(get_gromacs_energies(state, _monolithic=False))

openff/interchange/_tests/interoperability_tests/gromacs/__init__.py

@@ -0,0 +1 @@
+"""Interoperability tests with GROMACS."""

openff/interchange/_tests/interoperability_tests/gromacs/test_systems.py

@@ -1,6 +1,6 @@
 from openff.toolkit import Quantity
 
-from openff.interchange._tests._gromacs import gmx_monolithic_vs_itp
+from openff.interchange._tests._gromacs import gmx_monolithic_vs_itp, gmx_roundtrip
 
 
 def test_ligand_vacuum(caffeine, sage_unconstrained, monkeypatch):
@@ -9,16 +9,19 @@ def test_ligand_vacuum(caffeine, sage_unconstrained, monkeypatch):
     topology = caffeine.to_topology()
     topology.box_vectors = Quantity([4, 4, 4], "nanometer")
 
+    gmx_roundtrip(sage_unconstrained.create_interchange(topology))
     gmx_monolithic_vs_itp(sage_unconstrained.create_interchange(topology))
 
 
 def test_water_dimer(water_dimer, tip3p, monkeypatch):
     monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
 
+    gmx_roundtrip(tip3p.create_interchange(water_dimer))
     gmx_monolithic_vs_itp(tip3p.create_interchange(water_dimer))
 
 
 def test_alanine_dipeptide(alanine_dipeptide, ff14sb, monkeypatch):
     monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
 
+    gmx_roundtrip(ff14sb.create_interchange(alanine_dipeptide))
     gmx_monolithic_vs_itp(ff14sb.create_interchange(alanine_dipeptide))

openff/interchange/_tests/unit_tests/drivers/test_openmm.py

@@ -99,10 +99,6 @@ class TestReportWithPlugins:
     pytest.importorskip("smirnoff_plugins")
     pytest.importorskip("openeye")
 
-    @pytest.fixture
-    def ligand(self):
-        return MoleculeWithConformer.from_smiles("CC[C@@](/C=C\\[H])(C=C)O")
-
     @pytest.fixture
     def de_force_field(self) -> ForceField:
         return ForceField(

openff/interchange/components/mdconfig.py

@@ -462,12 +462,15 @@ def _infer_constraints(interchange: "Interchange") -> str:
 
             if num_constraints == num_h_bonds:
                 return "h-bonds"
-            elif num_constraints == len(interchange["Bonds"].key_map):
+            elif num_constraints == num_bonds:
                 return "all-bonds"
             elif num_constraints == (num_bonds + num_angles):
                 return "all-angles"
 
             else:
+                # TODO: Rigid waters may not have bond and angle parameters, but still have 3 constraints
+                #       per molecule. There should be a better way to process these, but it's non-trivial
+                #       to detect water molecules in a performance, scalable way without false positives.
                 warnings.warn(
                     "Ambiguous failure while processing constraints. Constraining h-bonds as a stopgap.",
                 )

openff/interchange/drivers/__init__.py

@@ -5,8 +5,10 @@
 from openff.interchange.drivers.gromacs import get_gromacs_energies
 from openff.interchange.drivers.lammps import get_lammps_energies
 from openff.interchange.drivers.openmm import get_openmm_energies
+from openff.interchange.drivers.report import EnergyReport
 
 __all__ = [
+    "EnergyReport",
     "get_all_energies",
     "get_amber_energies",
     "get_gromacs_energies",