def test_unpack_stored_simulation_data():
"""A test that compatible simulation data gets merged
together within the`LocalStorage` system."""
with tempfile.TemporaryDirectory() as directory:
force_field_path = os.path.join(directory, 'ff.json')
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
dummy_substance = create_dummy_substance(1)
dummy_directory_path = os.path.join(directory, 'data')
dummy_data_path = os.path.join(directory, 'data.json')
data_coordinate_name = 'data_1.pdb'
data_object = create_dummy_stored_simulation_data(
directory_path=dummy_directory_path,
substance=dummy_substance,
force_field_id='ff_id_1',
coordinate_file_name=data_coordinate_name,
statistical_inefficiency=1.0)
with open(dummy_data_path, 'w') as file:
json.dump(data_object, file, cls=TypedJSONEncoder)
unpack_stored_data = UnpackStoredSimulationData('unpack_data')
unpack_stored_data.simulation_data_path = (dummy_data_path,
dummy_directory_path,
force_field_path)
result = unpack_stored_data.execute(directory, None)
assert not isinstance(result, PropertyEstimatorException)
def test_unpack_stored_data_collection():
with tempfile.TemporaryDirectory() as directory:
force_field_path = os.path.join(directory, 'ff.json')
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
dummy_substance = create_dummy_substance(1)
data_collection_directory = os.path.join(directory,
f'dummy_collection')
os.makedirs(data_collection_directory, exist_ok=True)
dummy_data_collection = StoredDataCollection()
dummy_data_collection.substance = dummy_substance
dummy_data_collection.force_field_id = 'ff_id'
for inner_data_index in range(2):
data_key = f'data_{inner_data_index}'
data_path = os.path.join(data_collection_directory, data_key)
data_coordinate_name = f'data_{inner_data_index}.pdb'
inner_data = create_dummy_stored_simulation_data(
directory_path=data_path,
substance=dummy_substance,
force_field_id=f'ff_id',
coordinate_file_name=data_coordinate_name,
statistical_inefficiency=1.0)
dummy_data_collection.data[data_key] = inner_data
dummy_data_path = os.path.join(directory, 'data_collection.json')
with open(dummy_data_path, 'w') as file:
json.dump(dummy_data_collection, file, cls=TypedJSONEncoder)
unpack_data_collection = UnpackStoredDataCollection(
f'unpack_data_collection')
unpack_data_collection.input_data_path = (dummy_data_path,
data_collection_directory,
force_field_path)
result = unpack_data_collection.execute(directory, None)
assert not isinstance(result, PropertyEstimatorException)
def test_calculate_reduced_potential_openmm():
substance = Substance.from_components('O')
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, 'ff.json')
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
build_coordinates = BuildCoordinatesPackmol('build_coordinates')
build_coordinates.max_molecules = 10
build_coordinates.mass_density = 0.05 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildSmirnoffSystem(f'assign_parameters')
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
reduced_potentials = CalculateReducedPotentialOpenMM(f'reduced_potentials')
reduced_potentials.substance = substance
reduced_potentials.thermodynamic_state = thermodynamic_state
reduced_potentials.reference_force_field_paths = [force_field_path]
reduced_potentials.system_path = assign_parameters.system_path
reduced_potentials.trajectory_file_path = get_data_filename('test/trajectories/water.dcd')
reduced_potentials.coordinate_file_path = get_data_filename('test/trajectories/water.pdb')
reduced_potentials.kinetic_energies_path = get_data_filename('test/statistics/stats_pandas.csv')
reduced_potentials.high_precision = False
result = reduced_potentials.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert path.isfile(reduced_potentials.statistics_file_path)
final_array = StatisticsArray.from_pandas_csv(reduced_potentials.statistics_file_path)
assert ObservableType.ReducedPotential in final_array
def _setup_dummy_system(directory):
force_field_path = path.join(directory, 'ff.json')
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
substance = Substance.from_components('C')
build_coordinates = BuildCoordinatesPackmol('build_coordinates')
build_coordinates.max_molecules = 1
build_coordinates.mass_density = 0.001 * unit.grams / unit.milliliters
build_coordinates.substance = substance
build_coordinates.execute(directory, None)
assign_parameters = BuildSmirnoffSystem(f'assign_parameters')
assign_parameters.force_field_path = force_field_path
assign_parameters.coordinate_file_path = build_coordinates.coordinate_file_path
assign_parameters.substance = substance
assign_parameters.execute(directory, None)
return build_coordinates.coordinate_file_path, assign_parameters.system_path
def test_gradient_reduced_potentials(use_subset):
substance = Substance.from_components('O')
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
force_field_path = path.join(directory, 'ff.json')
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
reduced_potentials = GradientReducedPotentials(f'reduced_potentials')
reduced_potentials.substance = substance
reduced_potentials.thermodynamic_state = thermodynamic_state
reduced_potentials.reference_force_field_paths = [force_field_path]
reduced_potentials.reference_statistics_path = get_data_filename(
'test/statistics/stats_pandas.csv')
reduced_potentials.force_field_path = force_field_path
reduced_potentials.trajectory_file_path = get_data_filename(
'test/trajectories/water.dcd')
reduced_potentials.coordinate_file_path = get_data_filename(
'test/trajectories/water.pdb')
reduced_potentials.use_subset_of_force_field = use_subset
reduced_potentials.enable_pbc = True
reduced_potentials.parameter_key = ParameterGradientKey(
'vdW', '[#1]-[#8X2H2+0:1]-[#1]', 'epsilon')
result = reduced_potentials.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert path.isfile(reduced_potentials.forward_potentials_path)
assert path.isfile(reduced_potentials.reverse_potentials_path)
for reference_path in reduced_potentials.reference_force_field_paths:
assert path.isfile(reference_path)
def test_ligand_receptor_yank_protocol():
full_substance = Substance()
full_substance.add_component(
Substance.Component(smiles='c1ccccc1',
role=Substance.ComponentRole.Receptor),
Substance.ExactAmount(1))
full_substance.add_component(
Substance.Component(smiles='C', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
full_substance.add_component(
Substance.Component(smiles='O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
solute_substance = Substance()
solute_substance.add_component(
Substance.Component(smiles='C', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
solute_substance.add_component(
Substance.Component(smiles='O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
thermodynamic_state = ThermodynamicState(temperature=298.15 * unit.kelvin,
pressure=1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
with temporarily_change_directory(directory):
force_field_path = 'ff.json'
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
complex_coordinate_path, complex_system_path = _setup_dummy_system(
'full', full_substance, 3, force_field_path)
ligand_coordinate_path, ligand_system_path = _setup_dummy_system(
'ligand', solute_substance, 2, force_field_path)
run_yank = LigandReceptorYankProtocol('yank')
run_yank.substance = full_substance
run_yank.thermodynamic_state = thermodynamic_state
run_yank.number_of_iterations = 1
run_yank.steps_per_iteration = 1
run_yank.checkpoint_interval = 1
run_yank.verbose = True
run_yank.setup_only = True
run_yank.ligand_residue_name = 'TMP'
run_yank.receptor_residue_name = 'TMP'
run_yank.solvated_ligand_coordinates = ligand_coordinate_path
run_yank.solvated_ligand_system = ligand_system_path
run_yank.solvated_complex_coordinates = complex_coordinate_path
run_yank.solvated_complex_system = complex_system_path
run_yank.force_field_path = force_field_path
result = run_yank.execute('', ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
def test_solvation_yank_protocol(solvent_smiles):
full_substance = Substance()
full_substance.add_component(
Substance.Component(smiles='CO', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
full_substance.add_component(
Substance.Component(smiles=solvent_smiles,
role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
solvent_substance = Substance()
solvent_substance.add_component(
Substance.Component(smiles=solvent_smiles,
role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
solute_substance = Substance()
solute_substance.add_component(
Substance.Component(smiles='CO', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
thermodynamic_state = ThermodynamicState(temperature=298.15 * unit.kelvin,
pressure=1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
with temporarily_change_directory(directory):
force_field_path = 'ff.json'
with open(force_field_path, 'w') as file:
file.write(build_tip3p_smirnoff_force_field().json())
solvated_coordinate_path, solvated_system_path = _setup_dummy_system(
'full', full_substance, 2, force_field_path)
vacuum_coordinate_path, vacuum_system_path = _setup_dummy_system(
'vacuum', solute_substance, 1, force_field_path)
run_yank = SolvationYankProtocol('yank')
run_yank.solute = solute_substance
run_yank.solvent_1 = solvent_substance
run_yank.solvent_2 = Substance()
run_yank.thermodynamic_state = thermodynamic_state
run_yank.number_of_iterations = 1
run_yank.steps_per_iteration = 1
run_yank.checkpoint_interval = 1
run_yank.verbose = True
run_yank.setup_only = True
run_yank.solvent_1_coordinates = solvated_coordinate_path
run_yank.solvent_1_system = solvated_system_path
run_yank.solvent_2_coordinates = vacuum_coordinate_path
run_yank.solvent_2_system = vacuum_system_path
run_yank.electrostatic_lambdas_1 = [1.00]
run_yank.steric_lambdas_1 = [1.00]
run_yank.electrostatic_lambdas_2 = [1.00]
run_yank.steric_lambdas_2 = [1.00]
result = run_yank.execute('', ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
def test_base_simulation_protocols():
"""Tests that the commonly chain build coordinates, assigned topology,
energy minimise and perform simulation are able to work together without
raising an exception."""
water_substance = Substance()
water_substance.add_component(Substance.Component(smiles='O'),
Substance.MoleFraction())
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1 * unit.atmosphere)
with tempfile.TemporaryDirectory() as temporary_directory:
force_field_source = build_tip3p_smirnoff_force_field()
force_field_path = path.join(temporary_directory, 'ff.offxml')
with open(force_field_path, 'w') as file:
file.write(force_field_source.json())
build_coordinates = BuildCoordinatesPackmol('')
# Set the maximum number of molecules in the system.
build_coordinates.max_molecules = 10
# and the target density (the default 1.0 g/ml is normally fine)
build_coordinates.mass_density = 0.05 * unit.grams / unit.milliliters
# and finally the system which coordinates should be generated for.
build_coordinates.substance = water_substance
# Build the coordinates, creating a file called output.pdb
result = build_coordinates.execute(temporary_directory, None)
assert not isinstance(result, PropertyEstimatorException)
# Assign some smirnoff force field parameters to the
# coordinates
print('Assigning some parameters.')
assign_force_field_parameters = BuildSmirnoffSystem('')
assign_force_field_parameters.force_field_path = force_field_path
assign_force_field_parameters.coordinate_file_path = path.join(
temporary_directory, 'output.pdb')
assign_force_field_parameters.substance = water_substance
result = assign_force_field_parameters.execute(temporary_directory,
None)
assert not isinstance(result, PropertyEstimatorException)
# Do a simple energy minimisation
print('Performing energy minimisation.')
energy_minimisation = RunEnergyMinimisation('')
energy_minimisation.input_coordinate_file = path.join(
temporary_directory, 'output.pdb')
energy_minimisation.system_path = assign_force_field_parameters.system_path
result = energy_minimisation.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
npt_equilibration = RunOpenMMSimulation('npt_equilibration')
npt_equilibration.ensemble = Ensemble.NPT
npt_equilibration.steps_per_iteration = 20 # Debug settings.
npt_equilibration.output_frequency = 2 # Debug settings.
npt_equilibration.thermodynamic_state = thermodynamic_state
npt_equilibration.input_coordinate_file = path.join(
temporary_directory, 'minimised.pdb')
npt_equilibration.system_path = assign_force_field_parameters.system_path
result = npt_equilibration.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
extract_density = ExtractAverageStatistic('extract_density')
extract_density.statistics_type = ObservableType.Density
extract_density.statistics_path = path.join(temporary_directory,
'statistics.csv')
result = extract_density.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
extract_dielectric = ExtractAverageDielectric('extract_dielectric')
extract_dielectric.thermodynamic_state = thermodynamic_state
extract_dielectric.input_coordinate_file = path.join(
temporary_directory, 'input.pdb')
extract_dielectric.trajectory_path = path.join(temporary_directory,
'trajectory.dcd')
extract_dielectric.system_path = assign_force_field_parameters.system_path
result = extract_dielectric.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
extract_uncorrelated_trajectory = ExtractUncorrelatedTrajectoryData(
'extract_traj')
extract_uncorrelated_trajectory.statistical_inefficiency = extract_density.statistical_inefficiency
extract_uncorrelated_trajectory.equilibration_index = extract_density.equilibration_index
extract_uncorrelated_trajectory.input_coordinate_file = path.join(
temporary_directory, 'input.pdb')
extract_uncorrelated_trajectory.input_trajectory_path = path.join(
temporary_directory, 'trajectory.dcd')
result = extract_uncorrelated_trajectory.execute(
temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
extract_uncorrelated_statistics = ExtractUncorrelatedStatisticsData(
'extract_stats')
extract_uncorrelated_statistics.statistical_inefficiency = extract_density.statistical_inefficiency
extract_uncorrelated_statistics.equilibration_index = extract_density.equilibration_index
extract_uncorrelated_statistics.input_statistics_path = path.join(
temporary_directory, 'statistics.csv')
result = extract_uncorrelated_statistics.execute(
temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)