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

@@ -0,0 +1,21 @@
+"""Helpers for testing GROMACS interoperability."""
+
+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_roundtrip(state: Interchange, apply_smirnoff_defaults: bool = False):
+    with temporary_cd():
+        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)
+
+        # 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).compare(get_gromacs_energies(new_state))

openff/interchange/_tests/conftest.py

@@ -287,6 +287,21 @@ def gbsa_force_field() -> ForceField:
     )
 
 
+@pytest.fixture
+def ff14sb() -> ForceField:
+    return ForceField("ff14sb_off_impropers_0.0.3.offxml")
+
+
+@pytest.fixture
+def ligand():
+    return MoleculeWithConformer.from_smiles("CC[C@@](/C=C\\[H])(C=C)O", allow_undefined_stereo=True)
+
+
+@pytest.fixture
+def caffeine():
+    return MoleculeWithConformer.from_smiles("Cn1cnc2c1c(=O)n(C)c(=O)n2C")
+
+
 @pytest.fixture
 def basic_top() -> Topology:
     topology = MoleculeWithConformer.from_smiles("C").to_topology()
@@ -469,27 +484,33 @@ def ethanol_top(ethanol):
 
 
 @pytest.fixture
-def mainchain_ala():
-    molecule = Molecule.from_file(
-        get_data_file_path("proteins/MainChain_ALA.sdf", "openff.toolkit"),
+def alanine_dipeptide() -> Topology:
+    return Topology.from_pdb(
+        get_data_file_path(
+            "proteins/MainChain_ALA_ALA.pdb",
+            "openff.toolkit",
+        ),
     )
-    molecule._add_default_hierarchy_schemes()
-    molecule.perceive_residues()
-    molecule.perceive_hierarchy()
-
-    return molecule
 
 
 @pytest.fixture
-def mainchain_arg():
-    molecule = Molecule.from_file(
-        get_data_file_path("proteins/MainChain_ARG.sdf", "openff.toolkit"),
-    )
-    molecule._add_default_hierarchy_schemes()
-    molecule.perceive_residues()
-    molecule.perceive_hierarchy()
+def mainchain_ala() -> Molecule:
+    return Topology.from_pdb(
+        get_data_file_path(
+            "proteins/MainChain_ALA.pdb",
+            "openff.toolkit",
+        ),
+    ).molecule(0)
 
-    return molecule
+
+@pytest.fixture
+def mainchain_arg() -> Molecule:
+    return Topology.from_pdb(
+        get_data_file_path(
+            "proteins/MainChain_ARG.pdb",
+            "openff.toolkit",
+        ),
+    ).molecule(0)
 
 
 @pytest.fixture

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

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

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

@@ -0,0 +1,24 @@
+from openff.toolkit import Quantity
+
+from openff.interchange._tests._gromacs import gmx_roundtrip
+
+
+def test_ligand_vacuum(caffeine, sage_unconstrained, monkeypatch):
+    monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
+
+    topology = caffeine.to_topology()
+    topology.box_vectors = Quantity([4, 4, 4], "nanometer")
+
+    gmx_roundtrip(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))
+
+
+def test_alanine_dipeptide(alanine_dipeptide, ff14sb, monkeypatch):
+    monkeypatch.setenv("INTERCHANGE_EXPERIMENTAL", "1")
+
+    gmx_roundtrip(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",