Rename utils file

OpenFreeEnergy · Sep 25, 2024 · 8ad6e9d · 8ad6e9d
1 parent bab16de
commit 8ad6e9d
Show file tree

Hide file tree

Showing 3 changed files with 24 additions and 24 deletions.
diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py
@@ -40,7 +40,7 @@
     OpenMMEngineSettings,
     OpenMMSolvationSettings,
 )
-from openfe_gromacs.protocols.gromacs_utils import system_creation
+from openfe_gromacs.protocols.gromacs_utils import create_systems
 
 logger = logging.getLogger(__name__)
 
@@ -800,15 +800,15 @@ def run(
             stateA_system,
             stateA_topology,
             stateA_positions,
-        ) = system_creation.create_openmm_system(
+        ) = create_systems.create_openmm_system(
             settings,
             solvent_comp,
             protein_comp,
             smc_components,
             shared_basepath,
         )
         # 3. Create the Interchange object
-        stateA_interchange = system_creation.create_interchange(
+        stateA_interchange = create_systems.create_interchange(
             stateA_system,
             stateA_topology,
             stateA_positions,

diff --git a/...rotocols/gromacs_utils/system_creation.py → ...protocols/gromacs_utils/create_systems.py b/...rotocols/gromacs_utils/system_creation.py → ...protocols/gromacs_utils/create_systems.py
diff --git a/openfe_gromacs/tests/protocols/test_system_creation.py b/openfe_gromacs/tests/protocols/test_system_creation.py
@@ -7,28 +7,28 @@
 from openmm.app import GromacsGroFile, GromacsTopFile
 
 from openfe_gromacs.protocols.gromacs_md.md_methods import GromacsMDProtocol
-from openfe_gromacs.protocols.gromacs_utils import system_creation
+from openfe_gromacs.protocols.gromacs_utils import create_systems
 
-# def test_interchange_gromacs(T4_protein_component, tmpdir):
-#     solvent = gufe.SolventComponent()
-#     smc_components = {}
-#     settings = GromacsMDProtocol.default_settings()
-#     omm_system, omm_topology, omm_positions = system_creation.create_openmm_system(
-#         settings, solvent, T4_protein_component, smc_components, tmpdir
-#     )
-#     omm_atom_names = [atom.name for atom in omm_topology.atoms()]
-#     interchange = system_creation.create_interchange(
-#         omm_system, omm_topology, omm_positions, smc_components
-#     )
-#     interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
-#     interchange.to_gro(f"{tmpdir}/test.gro")
-#     gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
-#     assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
-#     assert omm_atom_names == interchange_atom_names == gro_atom_names
-#
-#     # check a few atom names to ensure these are not empty sets
-#     for atom_name in ("HA", "CH3", "CA", "CB"):
-#         assert atom_name in interchange_atom_names
+def test_interchange_gromacs(T4_protein_component, tmpdir):
+    solvent = gufe.SolventComponent()
+    smc_components = {}
+    settings = GromacsMDProtocol.default_settings()
+    omm_system, omm_topology, omm_positions = create_systems.create_openmm_system(
+        settings, solvent, T4_protein_component, smc_components, tmpdir
+    )
+    omm_atom_names = [atom.name for atom in omm_topology.atoms()]
+    interchange = create_systems.create_interchange(
+        omm_system, omm_topology, omm_positions, smc_components
+    )
+    interchange_atom_names = [atom.name for atom in interchange.topology.atoms]
+    interchange.to_gro(f"{tmpdir}/test.gro")
+    gro_atom_names = GromacsGroFile(f"{tmpdir}/test.gro").atomNames
+    assert len(omm_atom_names) == len(interchange_atom_names) == len(gro_atom_names)
+    assert omm_atom_names == interchange_atom_names == gro_atom_names
+
+    # check a few atom names to ensure these are not empty sets
+    for atom_name in ("HA", "CH3", "CA", "CB"):
+        assert atom_name in interchange_atom_names
 
 
 def test_user_charges(ethane, tmpdir):