diff --git a/openfe_gromacs/protocols/gromacs_md/md_methods.py b/openfe_gromacs/protocols/gromacs_md/md_methods.py index b1fd3ec..e3a6cf8 100644 --- 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__) @@ -800,7 +800,7 @@ def run( stateA_system, stateA_topology, stateA_positions, - ) = system_creation.create_openmm_system( + ) = create_systems.create_openmm_system( settings, solvent_comp, protein_comp, @@ -808,7 +808,7 @@ def run( 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/openfe_gromacs/protocols/gromacs_utils/system_creation.py b/openfe_gromacs/protocols/gromacs_utils/create_systems.py similarity index 100% rename from openfe_gromacs/protocols/gromacs_utils/system_creation.py rename to openfe_gromacs/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 index b72d6af..a0b4f52 100644 --- 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):