Add other test back in

OpenFreeEnergy · Sep 30, 2024 · f269ff6 · f269ff6
1 parent 839130e
commit f269ff6
Showing 1 changed file with 36 additions and 36 deletions.
diff --git a/openfe_gromacs/tests/protocols/test_create_systems.py b/openfe_gromacs/tests/protocols/test_create_systems.py
@@ -58,39 +58,39 @@ def test_interchange_gromacs(alanine_dipeptide_component, tmpdir):
         assert atom_name in interchange_atom_names
 
 
-# def test_user_charges(CN_molecule, tmpdir):
-#     solvent = gufe.SolventComponent()
-#     off_cn = CN_molecule.to_openff()
-#     off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
-#     off_charges = off_cn.partial_charges
-#     prot_settings = GromacsMDProtocol.default_settings()
-#     smc_components = {CN_molecule: off_cn}
-#     omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
-#         solvent,
-#         None,
-#         smc_components,
-#         prot_settings.partial_charge_settings,
-#         prot_settings.forcefield_settings,
-#         prot_settings.integrator_settings,
-#         prot_settings.thermo_settings,
-#         prot_settings.solvation_settings,
-#         prot_settings.output_settings_em,
-#         tmpdir,
-#     )
-#
-#     interchange = create_systems.create_interchange(
-#         omm_system, omm_topology, omm_positions, smc_components
-#     )
-#     # Save to Gromacs .top file
-#     interchange.to_top(f"{tmpdir}/test.top")
-#     # Load Gromacs .top file back in as OpenMM system
-#     gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
-#     # Get the partial charges of the ligand atoms
-#     nonbonded = [
-#         f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
-#     ][0]
-#     gro_charges = []
-#     for i in range(len(off_charges)):
-#         charge, sigma, epsilon = nonbonded.getParticleParameters(i)
-#         gro_charges.append(charge._value)
-#     np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)
+def test_user_charges(CN_molecule, tmpdir):
+    solvent = gufe.SolventComponent()
+    off_cn = CN_molecule.to_openff()
+    off_cn.assign_partial_charges(partial_charge_method="am1-mulliken")
+    off_charges = off_cn.partial_charges
+    prot_settings = GromacsMDProtocol.default_settings()
+    smc_components = {CN_molecule: off_cn}
+    omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
+        solvent,
+        None,
+        smc_components,
+        prot_settings.partial_charge_settings,
+        prot_settings.forcefield_settings,
+        prot_settings.integrator_settings,
+        prot_settings.thermo_settings,
+        prot_settings.solvation_settings,
+        prot_settings.output_settings_em,
+        tmpdir,
+    )
+
+    interchange = create_systems.create_interchange(
+        omm_system, omm_topology, omm_positions, smc_components
+    )
+    # Save to Gromacs .top file
+    interchange.to_top(f"{tmpdir}/test.top")
+    # Load Gromacs .top file back in as OpenMM system
+    gromacs_system = GromacsTopFile(f"{tmpdir}/test.top").createSystem()
+    # Get the partial charges of the ligand atoms
+    nonbonded = [
+        f for f in gromacs_system.getForces() if isinstance(f, NonbondedForce)
+    ][0]
+    gro_charges = []
+    for i in range(len(off_charges)):
+        charge, sigma, epsilon = nonbonded.getParticleParameters(i)
+        gro_charges.append(charge._value)
+    np.testing.assert_almost_equal(off_charges.m, gro_charges, decimal=5)