Merge pull request #762 from openforcefield/fixtures

Reconfigure common objects into fixtures

devtools/conda-envs/dev_env.yaml

@@ -27,6 +27,7 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-xdist
+  - pytest-randomly
   - nbval
   - qcportal
   - openff-qcsubmit

openff/interchange/_tests/__init__.py

@@ -7,10 +7,9 @@
 import numpy as np
 import openmm
 import pytest
-from openff.toolkit._tests.create_molecules import create_ammonia, create_ethanol
+from openff.toolkit import ForceField, Molecule, Topology
+from openff.toolkit._tests.create_molecules import create_ethanol
 from openff.toolkit._tests.utils import get_data_file_path
-from openff.toolkit.topology import Molecule, Topology
-from openff.toolkit.typing.engines.smirnoff import ForceField
 from openff.units import unit
 from openff.utilities.utilities import has_executable
 from openmm import unit as openmm_unit
@@ -55,36 +54,23 @@ def get_test_files_dir_path(dirname: Optional[str] = None) -> pathlib.Path:
         )
 
 
-class _BaseTest:
-    @pytest.fixture(autouse=True)
-    def _initdir(self, tmpdir):
-        tmpdir.chdir()
+class MoleculeWithConformer(Molecule):
+    """Thin wrapper around `Molecule` to produce an instance with a conformer in one call."""
 
-    # TODO: group fixtures up as dicts, i.e. argon['forcefield'], argon['topology'], ...
-    @pytest.fixture()
-    def argon_ff(self):
-        """Fixture that loads an SMIRNOFF XML for argon."""
-        return ForceField(get_test_file_path("argon.offxml"))
+    @classmethod
+    def from_smiles(self, smiles, name=""):
+        """Create from smiles and generate a single conformer."""
+        molecule = super().from_smiles(smiles)
+        molecule.generate_conformers(n_conformers=1)
+        molecule.name = name
 
-    @pytest.fixture()
-    def argon(self):
-        """Fixture that builds a simple arogon topology."""
-        argon = Molecule()
-        argon.add_atom(
-            atomic_number=18,
-            formal_charge=0,
-            is_aromatic=False,
-        )
-        return argon
+        return molecule
 
-    @pytest.fixture()
-    def ammonia_ff(self):
-        """Fixture that loads an SMIRNOFF XML for ammonia."""
-        return ForceField(get_test_file_path("ammonia.offxml"))
 
-    @pytest.fixture()
-    def ammonia(self):
-        return create_ammonia()
+class _BaseTest:
+    @pytest.fixture(autouse=True)
+    def _initdir(self, tmpdir):
+        tmpdir.chdir()
 
     @pytest.fixture()
     def ethanol(self):
@@ -96,11 +82,6 @@ def basic_top(self):
         top.box_vectors = unit.Quantity([5, 5, 5], unit.nanometer)
         return top
 
-    @pytest.fixture()
-    def ammonia_top(self, ammonia):
-        """Fixture that builds a simple ammonia topology."""
-        return Topology.from_molecules(4 * [ammonia])
-
     @pytest.fixture()
     def ethanol_top(self, ethanol):
         """Fixture that builds a simple four ethanol topology."""
@@ -136,105 +117,6 @@ def mainchain_arg(self):
     def two_peptides(self, mainchain_ala, mainchain_arg):
         return Topology.from_molecules([mainchain_ala, mainchain_arg])
 
-    @pytest.fixture()
-    def tip3p_xml(self):
-        # Modified (added Electrostatics tag) from below link
-        # https://github.com/openforcefield/openff-toolkit/blob/0.10.2/openff/toolkit/data/test_forcefields/tip3p.offxml
-        return """<?xml version="1.0" encoding='ASCII'?>
-<SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
-  <Constraints version="0.3">
-    <Constraint smirks="[#1:1]-[*:2]" id="c1"></Constraint>
-    <Constraint smirks="[#1:1]-[#8X2H2+0:2]-[#1]"
-        id="c-tip3p-H-O" distance="0.9572 * angstrom"></Constraint>
-    <Constraint smirks="[#1:1]-[#8X2H2+0]-[#1:2]"
-        id="c-tip3p-H-O-H" distance="1.5139006545247014*angstrom"></Constraint>
-  </Constraints>
-  <vdW
-    version="0.3"
-    potential="Lennard-Jones-12-6"
-    combining_rules="Lorentz-Berthelot"
-    scale12="0.0"
-    scale13="0.0"
-    scale14="0.5"
-    scale15="1"
-    switch_width="1.0*angstroms"
-    cutoff="9.0*angstroms" method="cutoff"
-  >
-    <Atom
-      smirks="[#1]-[#8X2H2+0:1]-[#1]"
-      id="n1"
-      sigma="0.31507524065751241*nanometers"
-      epsilon="0.635968*kilojoules_per_mole"
-    />
-    <Atom
-      smirks="[#1:1]-[#8X2H2+0]-[#1]"
-      id="n2"
-      sigma="1*nanometers"
-      epsilon="0*kilojoules_per_mole" />
-  </vdW>
-  <Electrostatics
-    version="0.3"
-    method="PME"
-    scale12="0.0"
-    scale13="0.0"
-    scale14="0.833333"
-    scale15="1.0"
-    switch_width="0.0*angstrom"
-    cutoff="9.0*angstrom"
-  ></Electrostatics>
-  <LibraryCharges version="0.3">
-    <LibraryCharge
-        name="TIP3P"
-        smirks="[#1:1]-[#8X2H2+0:2]-[#1:3]"
-        charge1="0.417*elementary_charge"
-        charge2="-0.834*elementary_charge"
-        charge3="0.417*elementary_charge"/>
-  </LibraryCharges>
-</SMIRNOFF>"""
-
-    @pytest.fixture()
-    def tip3p(self, tip3p_xml):
-        return ForceField(tip3p_xml)
-
-    @pytest.fixture()
-    def tip3p_missing_electrostatics_xml(self):
-        # Stripped from below, follow link for details
-        # https://github.com/openforcefield/openff-toolkit/blob/0.10.2/openff/toolkit/data/test_forcefields/tip3p.offxml
-        return """<?xml version="1.0" encoding='ASCII'?>
-<SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
-  <vdW
-    version="0.3"
-    potential="Lennard-Jones-12-6"
-    combining_rules="Lorentz-Berthelot"
-    scale12="0.0"
-    scale13="0.0"
-    scale14="0.5"
-    scale15="1"
-    switch_width="1.0*angstroms"
-    cutoff="9.0*angstroms" method="cutoff"
-  >
-    <Atom
-      smirks="[#1]-[#8X2H2+0:1]-[#1]"
-      id="n1"
-      sigma="0.31507524065751241*nanometers"
-      epsilon="0.635968*kilojoules_per_mole"
-    />
-    <Atom
-      smirks="[#1:1]-[#8X2H2+0]-[#1]"
-      id="n2"
-      sigma="1*nanometers"
-      epsilon="0*kilojoules_per_mole" />
-  </vdW>
-  <LibraryCharges version="0.3">
-    <LibraryCharge
-        name="TIP3P"
-        smirks="[#1:1]-[#8X2H2+0:2]-[#1:3]"
-        charge1="0.417*elementary_charge"
-        charge2="-0.834*elementary_charge"
-        charge3="0.417*elementary_charge"/>
-  </LibraryCharges>
-</SMIRNOFF>"""
-
     xml_ff_bo_bonds = """<?xml version='1.0' encoding='ASCII'?>
     <SMIRNOFF version="0.3" aromaticity_model="OEAroModel_MDL">
       <Bonds version="0.3" fractional_bondorder_method="AM1-Wiberg" fractional_bondorder_interpolation="linear">
@@ -284,10 +166,6 @@ def acetaldehyde(self):
             "[C:1]([C:2](=[O:3])[H:7])([H:4])([H:5])[H:6]",
         )
 
-    @pytest.fixture()
-    def water(self):
-        return Molecule.from_mapped_smiles("[H:2][O:1][H:3]")
-
 
 HAS_GROMACS = _find_gromacs_executable() is not None
 HAS_LAMMPS = _find_lammps_executable() is not None

openff/interchange/_tests/conftest.py

@@ -0,0 +1,36 @@
+"""Pytest configuration."""
+import pytest
+from openff.toolkit import ForceField, Molecule
+
+from openff.interchange._tests import get_test_file_path
+
+
+@pytest.fixture()
+def _simple_force_field():
+    # TODO: Create a minimal force field for faster tests
+    pass
+
+
+@pytest.fixture()
+def tip3p() -> ForceField:
+    return ForceField("tip3p.offxml")
+
+
+@pytest.fixture()
+def tip4p() -> ForceField:
+    return ForceField("tip4p_fb.offxml")
+
+
+@pytest.fixture()
+def gbsa_force_field() -> ForceField:
+    return ForceField(
+        "openff-2.0.0.offxml",
+        get_test_file_path("gbsa.offxml"),
+    )
+
+
+@pytest.fixture(scope="session")
+def water() -> Molecule:
+    molecule = Molecule.from_mapped_smiles("[H:2][O:1][H:3]")
+    molecule.generate_conformers(n_conformers=1)
+    return molecule

openff/interchange/_tests/energy_tests/components/tests_smirnoff.py

@@ -1,9 +1,8 @@
 import numpy as np
 import openmm
 import pytest
+from openff.toolkit import ForceField, Molecule
 from openff.toolkit._tests.utils import get_data_file_path
-from openff.toolkit.topology import Molecule
-from openff.toolkit.typing.engines.smirnoff.forcefield import ForceField
 from openff.units import unit
 from openmm import unit as openmm_unit
 

openff/interchange/_tests/energy_tests/test_energies.py

@@ -11,6 +11,7 @@
 from openff.interchange._tests import (
     HAS_GROMACS,
     HAS_LAMMPS,
+    MoleculeWithConformer,
     _BaseTest,
     get_test_file_path,
     needs_gmx,
@@ -45,17 +46,15 @@ def oplsaa(self):
     def test_energies_single_mol(self, constrained, sage, sage_unconstrained, mol_smi):
         import mbuild as mb
 
-        mol = Molecule.from_smiles(mol_smi)
-        mol.generate_conformers(n_conformers=1)
-        mol.name = "FOO"
+        molecule = MoleculeWithConformer.from_smiles(mol_smi, name="FOO")
 
         force_field = sage if constrained else sage_unconstrained
 
-        interchange = Interchange.from_smirnoff(force_field, [mol])
+        interchange = Interchange.from_smirnoff(force_field, [molecule])
 
         interchange.collections["Electrostatics"].periodic_potential = "cutoff"
 
-        mol.to_file("out.xyz", file_format="xyz")
+        molecule.to_file("out.xyz", file_format="xyz")
         compound = mb.load("out.xyz")
         packed_box = mb.fill_box(
             compound=compound,
@@ -107,8 +106,7 @@ def test_process_rb_torsions(self, oplsaa):
 
         from openff.interchange.components.mbuild import offmol_to_compound
 
-        ethanol = Molecule.from_smiles("CCO")
-        ethanol.generate_conformers(n_conformers=1)
+        ethanol = MoleculeWithConformer.from_smiles("CCO")
         ethanol.generate_unique_atom_names()
 
         my_compound = offmol_to_compound(ethanol)
@@ -136,9 +134,7 @@ def test_gmx_14_energies_exist(self, sage):
 
         # Use a molecule with only one 1-4 interaction, and
         # make it between heavy atoms because H-H 1-4 are weak
-        mol = Molecule.from_smiles("ClC#CCl")
-        mol.name = "HPER"
-        mol.generate_conformers(n_conformers=1)
+        mol = MoleculeWithConformer.from_smiles("ClC#CCl", name="HPER")
 
         out = Interchange.from_smirnoff(sage, [mol])
         out.positions = mol.conformers[0]
@@ -215,17 +211,16 @@ def test_interpolated_parameters(self, smi):
         </SMIRNOFF>
         """
 
-        mol = Molecule.from_smiles(smi)
-        mol.generate_conformers(n_conformers=1)
+        molecule = MoleculeWithConformer.from_smiles(smi)
 
         forcefield = ForceField(
             "openff-2.0.0.offxml",
             xml_ff_bo_all_heavy_bonds,
         )
 
-        out = Interchange.from_smirnoff(forcefield, [mol])
+        out = Interchange.from_smirnoff(forcefield, [molecule])
         out.box = [4, 4, 4] * unit.nanometer
-        out.positions = mol.conformers[0]
+        out.positions = molecule.conformers[0]
 
         for key in ["Bond", "Torsion"]:
             interchange_energy = get_openmm_energies(