def test_solvate_existing_structure_protocol():
"""Tests solvating a single methanol molecule in water."""
methanol_substance = Substance()
methanol_substance.add_component(Substance.Component('CO'),
Substance.ExactAmount(1))
water_substance = Substance()
water_substance.add_component(Substance.Component('O'),
Substance.MoleFraction(1.0))
with tempfile.TemporaryDirectory() as temporary_directory:
build_methanol_coordinates = BuildCoordinatesPackmol('build_methanol')
build_methanol_coordinates.max_molecules = 1
build_methanol_coordinates.substance = methanol_substance
build_methanol_coordinates.execute(temporary_directory,
ComputeResources())
solvate_coordinates = SolvateExistingStructure('solvate_methanol')
solvate_coordinates.max_molecules = 9
solvate_coordinates.substance = water_substance
solvate_coordinates.solute_coordinate_file = build_methanol_coordinates.coordinate_file_path
solvate_coordinates.execute(temporary_directory, ComputeResources())
solvated_pdb = PDBFile(solvate_coordinates.coordinate_file_path)
assert solvated_pdb.topology.getNumResidues() == 10
def test_addition_subtract_protocols():
with tempfile.TemporaryDirectory() as temporary_directory:
quantity_a = EstimatedQuantity(1 * unit.kelvin, 0.1 * unit.kelvin,
'dummy_source_1')
quantity_b = EstimatedQuantity(2 * unit.kelvin, 0.2 * unit.kelvin,
'dummy_source_2')
add_quantities = AddQuantities('add')
add_quantities.values = [quantity_a, quantity_b]
result = add_quantities.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert add_quantities.result.value == 3 * unit.kelvin
sub_quantities = SubtractQuantities('sub')
sub_quantities.value_b = quantity_b
sub_quantities.value_a = quantity_a
result = sub_quantities.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert sub_quantities.result.value == 1 * unit.kelvin
def test_run_openmm_simulation_checkpoints():
import mdtraj
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
coordinate_path, system_path = _setup_dummy_system(directory)
# Check that executing twice doesn't run the simulation twice
npt_equilibration = RunOpenMMSimulation('npt_equilibration')
npt_equilibration.total_number_of_iterations = 1
npt_equilibration.steps_per_iteration = 4
npt_equilibration.output_frequency = 1
npt_equilibration.thermodynamic_state = thermodynamic_state
npt_equilibration.input_coordinate_file = coordinate_path
npt_equilibration.system_path = system_path
npt_equilibration.execute(directory, ComputeResources())
assert os.path.isfile(npt_equilibration._checkpoint_path)
npt_equilibration.execute(directory, ComputeResources())
assert len(
StatisticsArray.from_pandas_csv(
npt_equilibration.statistics_file_path)) == 4
assert len(
mdtraj.load(npt_equilibration.trajectory_file_path,
top=coordinate_path)) == 4
# Make sure that the output files are correctly truncating if more frames
# than expected are written
with open(npt_equilibration._checkpoint_path, 'r') as file:
checkpoint = json.load(file, cls=TypedJSONDecoder)
# Fake having saved more frames than expected
npt_equilibration.steps_per_iteration = 8
checkpoint.steps_per_iteration = 8
npt_equilibration.output_frequency = 2
checkpoint.output_frequency = 2
with open(npt_equilibration._checkpoint_path, 'w') as file:
json.dump(checkpoint, file, cls=TypedJSONEncoder)
npt_equilibration.execute(directory, ComputeResources())
assert len(
StatisticsArray.from_pandas_csv(
npt_equilibration.statistics_file_path)) == 4
assert len(
mdtraj.load(npt_equilibration.trajectory_file_path,
top=coordinate_path)) == 4
def main(n_workers, cpus_per_worker, gpus_per_worker):
if n_workers <= 0:
raise ValueError('The number of workers must be greater than 0')
if cpus_per_worker <= 0:
raise ValueError('The number of CPU\'s per worker must be greater than 0')
if gpus_per_worker < 0:
raise ValueError('The number of GPU\'s per worker must be greater than or equal to 0')
if 0 < gpus_per_worker != cpus_per_worker:
raise ValueError('The number of GPU\'s per worker must match the number of '
'CPU\'s per worker.')
# Set up logging for the propertyestimator.
setup_timestamp_logging()
logger = logging.getLogger()
# Set up the directory structure.
working_directory = 'working_directory'
storage_directory = 'storage_directory'
# Remove any existing data.
if path.isdir(working_directory):
shutil.rmtree(working_directory)
# Set up a backend to run the calculations on with the requested resources.
if gpus_per_worker <= 0:
worker_resources = ComputeResources(number_of_threads=cpus_per_worker)
else:
worker_resources = ComputeResources(number_of_threads=cpus_per_worker,
number_of_gpus=gpus_per_worker,
preferred_gpu_toolkit=QueueWorkerResources.GPUToolkit.CUDA)
calculation_backend = DaskLocalCluster(number_of_workers=n_workers,
resources_per_worker=worker_resources)
# Create a backend to cache simulation files.
storage_backend = LocalFileStorage(storage_directory)
# Create an estimation server which will run the calculations.
logger.info(f'Starting the server with {n_workers} workers, each with '
f'{cpus_per_worker} CPUs and {gpus_per_worker} GPUs.')
server = PropertyEstimatorServer(calculation_backend=calculation_backend,
storage_backend=storage_backend,
working_directory=working_directory,
port=8000)
# Tell the server to start listening for estimation requests.
server.start_listening_loop()
def test_substance_filtering_protocol(filter_role):
"""Tests that the protocol to filter substances by
role correctly works."""
def create_substance():
test_substance = Substance()
test_substance.add_component(Substance.Component('C', role=Substance.ComponentRole.Solute),
Substance.ExactAmount(1))
test_substance.add_component(Substance.Component('CC', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
test_substance.add_component(Substance.Component('CCC', role=Substance.ComponentRole.Receptor),
Substance.ExactAmount(1))
test_substance.add_component(Substance.Component('O', role=Substance.ComponentRole.Solvent),
Substance.MoleFraction(1.0))
return test_substance
filter_protocol = FilterSubstanceByRole('filter_protocol')
filter_protocol.input_substance = create_substance()
filter_protocol.component_role = filter_role
filter_protocol.execute('', ComputeResources())
assert len(filter_protocol.filtered_substance.components) == 1
assert filter_protocol.filtered_substance.components[0].role == filter_role
def test_reweight_statistics():
number_of_frames = 10
reduced_potentials = np.ones(number_of_frames) * random.random() * unit.dimensionless
potentials = np.ones(number_of_frames) * random.random() * unit.kilojoule / unit.mole
with tempfile.TemporaryDirectory() as directory:
statistics_path = path.join(directory, 'stats.csv')
statistics_array = StatisticsArray()
statistics_array[ObservableType.ReducedPotential] = reduced_potentials
statistics_array[ObservableType.PotentialEnergy] = potentials
statistics_array.to_pandas_csv(statistics_path)
reweight_protocol = ReweightStatistics(f'reduced_potentials')
reweight_protocol.statistics_type = ObservableType.PotentialEnergy
reweight_protocol.statistics_paths = [statistics_path]
reweight_protocol.reference_reduced_potentials = [statistics_path]
reweight_protocol.target_reduced_potentials = [statistics_path]
reweight_protocol.bootstrap_uncertainties = True
reweight_protocol.required_effective_samples = 0
result = reweight_protocol.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
def test_central_difference_gradient():
with tempfile.TemporaryDirectory() as directory:
gradient_key = ParameterGradientKey('vdW', '[#1]-[#8X2H2+0:1]-[#1]',
'epsilon')
reverse_parameter = -random.random() * unit.kelvin
reverse_observable = -random.random() * unit.kelvin
forward_parameter = random.random() * unit.kelvin
forward_observable = random.random() * unit.kelvin
central_difference = CentralDifferenceGradient('central_difference')
central_difference.parameter_key = gradient_key
central_difference.reverse_observable_value = reverse_observable
central_difference.reverse_parameter_value = reverse_parameter
central_difference.forward_observable_value = forward_observable
central_difference.forward_parameter_value = forward_parameter
result = central_difference.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert central_difference.gradient.value == (
(forward_observable - reverse_observable) /
(forward_parameter - reverse_parameter))
def test_extract_uncorrelated_trajectory_data():
import mdtraj
coordinate_path = get_data_filename('test/trajectories/water.pdb')
trajectory_path = get_data_filename('test/trajectories/water.dcd')
original_trajectory = mdtraj.load(trajectory_path, top=coordinate_path)
with tempfile.TemporaryDirectory() as temporary_directory:
extract_protocol = ExtractUncorrelatedTrajectoryData(
'extract_protocol')
extract_protocol.input_coordinate_file = coordinate_path
extract_protocol.input_trajectory_path = trajectory_path
extract_protocol.equilibration_index = 2
extract_protocol.statistical_inefficiency = 2.0
result = extract_protocol.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
final_trajectory = mdtraj.load(extract_protocol.output_trajectory_path,
top=coordinate_path)
assert len(final_trajectory) == (len(original_trajectory) - 2) / 2
assert extract_protocol.number_of_uncorrelated_samples == (
len(original_trajectory) - 2) / 2
def _get_options_dictionary(self, available_resources):
"""Returns a dictionary of options which will be serialized
to a yaml file and passed to YANK.
Parameters
----------
available_resources: ComputeResources
The resources available to execute on.
Returns
-------
dict of str and Any
A yaml compatible dictionary of YANK options.
"""
from openforcefield.utils import quantity_to_string
platform_name = 'CPU'
if available_resources.number_of_gpus > 0:
# A platform which runs on GPUs has been requested.
from propertyestimator.backends import ComputeResources
toolkit_enum = ComputeResources.GPUToolkit(
available_resources.preferred_gpu_toolkit)
# A platform which runs on GPUs has been requested.
platform_name = 'CUDA' if toolkit_enum == ComputeResources.GPUToolkit.CUDA else \
ComputeResources.GPUToolkit.OpenCL
return {
'verbose':
self.verbose,
'output_dir':
'.',
'temperature':
quantity_to_string(
pint_quantity_to_openmm(self.thermodynamic_state.temperature)),
'pressure':
quantity_to_string(
pint_quantity_to_openmm(self.thermodynamic_state.pressure)),
'minimize':
True,
'number_of_equilibration_iterations':
self.number_of_equilibration_iterations,
'default_number_of_iterations':
self.number_of_iterations,
'default_nsteps_per_iteration':
self.steps_per_iteration,
'checkpoint_interval':
self.checkpoint_interval,
'default_timestep':
quantity_to_string(pint_quantity_to_openmm(self.timestep)),
'annihilate_electrostatics':
True,
'annihilate_sterics':
False,
'platform':
platform_name
}
def test_nested_input():
dummy_schema = WorkflowSchema()
dict_protocol = DummyInputOutputProtocol('dict_protocol')
dict_protocol.input_value = {'a': ThermodynamicState(temperature=1*unit.kelvin)}
dummy_schema.protocols[dict_protocol.id] = dict_protocol.schema
quantity_protocol = DummyInputOutputProtocol('quantity_protocol')
quantity_protocol.input_value = ProtocolPath('output_value[a].temperature', dict_protocol.id)
dummy_schema.protocols[quantity_protocol.id] = quantity_protocol.schema
dummy_schema.validate_interfaces()
dummy_property = create_dummy_property(Density)
dummy_workflow = Workflow(dummy_property, {})
dummy_workflow.schema = dummy_schema
with tempfile.TemporaryDirectory() as temporary_directory:
workflow_graph = WorkflowGraph(temporary_directory)
workflow_graph.add_workflow(dummy_workflow)
dask_local_backend = DaskLocalCluster(1, ComputeResources(1))
dask_local_backend.start()
results_futures = workflow_graph.submit(dask_local_backend)
assert len(results_futures) == 1
result = results_futures[0].result()
assert isinstance(result, CalculationLayerResult)
def test_add_values_protocol(values):
with tempfile.TemporaryDirectory() as temporary_directory:
add_quantities = AddValues('add')
add_quantities.values = values
result = add_quantities.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert add_quantities.result == reduce(operator.add, values)
def test_subtract_values_protocol(values):
with tempfile.TemporaryDirectory() as temporary_directory:
sub_quantities = SubtractValues('sub')
sub_quantities.value_b = values[1]
sub_quantities.value_a = values[0]
result = sub_quantities.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert sub_quantities.result == values[1] - values[0]
def test_simple_workflow_graph_with_groups():
dummy_schema = WorkflowSchema()
dummy_protocol_a = DummyEstimatedQuantityProtocol('protocol_a')
dummy_protocol_a.input_value = EstimatedQuantity(1 * unit.kelvin,
0.1 * unit.kelvin,
'dummy_source')
dummy_protocol_b = DummyEstimatedQuantityProtocol('protocol_b')
dummy_protocol_b.input_value = ProtocolPath('output_value',
dummy_protocol_a.id)
conditional_group = ConditionalGroup('conditional_group')
conditional_group.add_protocols(dummy_protocol_a, dummy_protocol_b)
condition = ConditionalGroup.Condition()
condition.right_hand_value = 2 * unit.kelvin
condition.type = ConditionalGroup.ConditionType.LessThan
condition.left_hand_value = ProtocolPath('output_value.value',
conditional_group.id,
dummy_protocol_b.id)
conditional_group.add_condition(condition)
dummy_schema.protocols[conditional_group.id] = conditional_group.schema
dummy_schema.final_value_source = ProtocolPath('output_value',
conditional_group.id,
dummy_protocol_b.id)
dummy_schema.validate_interfaces()
dummy_property = create_dummy_property(Density)
dummy_workflow = Workflow(dummy_property, {})
dummy_workflow.schema = dummy_schema
with tempfile.TemporaryDirectory() as temporary_directory:
workflow_graph = WorkflowGraph(temporary_directory)
workflow_graph.add_workflow(dummy_workflow)
dask_local_backend = DaskLocalClusterBackend(1, ComputeResources(1))
dask_local_backend.start()
results_futures = workflow_graph.submit(dask_local_backend)
assert len(results_futures) == 1
result = results_futures[0].result()
assert isinstance(result, CalculationLayerResult)
assert result.calculated_property.value == 1 * unit.kelvin
def test_multiply_values_protocol(value, multiplier):
with tempfile.TemporaryDirectory() as temporary_directory:
multiply_quantities = MultiplyValue('multiply')
multiply_quantities.value = value
multiply_quantities.multiplier = multiplier
result = multiply_quantities.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert multiply_quantities.result == value * multiplier
def test_divide_values_protocol(value, divisor):
with tempfile.TemporaryDirectory() as temporary_directory:
divide_quantities = DivideValue('divide')
divide_quantities.value = value
divide_quantities.divisor = divisor
result = divide_quantities.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert divide_quantities.result == value / divisor
def test_extract_average_statistic():
statistics_path = get_data_filename('test/statistics/stats_pandas.csv')
with tempfile.TemporaryDirectory() as temporary_directory:
extract_protocol = ExtractAverageStatistic('extract_protocol')
extract_protocol.statistics_path = statistics_path
extract_protocol.statistics_type = ObservableType.PotentialEnergy
result = extract_protocol.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
def build_solvated_system():
"""An example of how to build a solvated system using the built in
utilities and protocol classes.
"""
# Define the system that you wish to create coordinates for.
mixed_system = Mixture()
# Here we simply define a 1:1 mix of water and octanol.
mixed_system.add_component(smiles='O', mole_fraction=0.5)
mixed_system.add_component(smiles='CCCCCCCCO', mole_fraction=0.5)
# Add any 'impurities' such as single solute molecules.
# In this case we add a molecule of paracetamol.
mixed_system.add_component(smiles='CC(=O)NC1=CC=C(C=C1)O', mole_fraction=0.0, impurity=True)
# Create an object which under the hood calls the packmol utility
# in a friendlier way:
print('Building the coordinates (this may take a while...)')
build_coordinates = BuildCoordinatesPackmol('')
# Set the maximum number of molecules in the system.
build_coordinates.max_molecules = 1500
# and the target density (the default 1.0 g/ml is normally fine)
build_coordinates.mass_density = 1.0 * unit.grams / unit.milliliters
# and finally the system which coordinates should be generated for.
build_coordinates.substance = mixed_system
# Build the coordinates, creating a file called output.pdb
build_coordinates.execute('', None)
# 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 = get_data_filename('forcefield/smirnoff99Frosst.offxml')
assign_force_field_parameters.coordinate_file_path = 'output.pdb'
assign_force_field_parameters.substance = mixed_system
assign_force_field_parameters.execute('', None)
# Do a simple energy minimisation
print('Performing energy minimisation.')
energy_minimisation = RunEnergyMinimisation('')
energy_minimisation.input_coordinate_file = 'output.pdb'
energy_minimisation.system_path = assign_force_field_parameters.system_path
energy_minimisation.execute('', ComputeResources())
def test_run_energy_minimisation():
with tempfile.TemporaryDirectory() as directory:
coordinate_path, system_path = _setup_dummy_system(directory)
energy_minimisation = RunEnergyMinimisation('energy_minimisation')
energy_minimisation.input_coordinate_file = coordinate_path
energy_minimisation.system_path = system_path
result = energy_minimisation.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert path.isfile(energy_minimisation.output_coordinate_file)
def test_concatenate_statistics():
statistics_path = get_data_filename('test/statistics/stats_pandas.csv')
original_array = StatisticsArray.from_pandas_csv(statistics_path)
with tempfile.TemporaryDirectory() as temporary_directory:
concatenate_protocol = ConcatenateStatistics('concatenate_protocol')
concatenate_protocol.input_statistics_paths = [statistics_path, statistics_path]
result = concatenate_protocol.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
final_array = StatisticsArray.from_pandas_csv(concatenate_protocol.output_statistics_path)
assert len(final_array) == len(original_array) * 2
def test_weight_by_mole_fraction_protocol(component_smiles, value):
full_substance = Substance.from_components('C', 'CC', 'CCC')
component = Substance.from_components(component_smiles)
mole_fraction = next(iter(full_substance.get_amounts(component_smiles))).value
with tempfile.TemporaryDirectory() as temporary_directory:
weight_protocol = WeightByMoleFraction('weight')
weight_protocol.value = value
weight_protocol.full_substance = full_substance
weight_protocol.component = component
result = weight_protocol.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert weight_protocol.weighted_value == value * mole_fraction
def test_concatenate_trajectories():
import mdtraj
coordinate_path = get_data_filename('test/trajectories/water.pdb')
trajectory_path = get_data_filename('test/trajectories/water.dcd')
original_trajectory = mdtraj.load(trajectory_path, top=coordinate_path)
with tempfile.TemporaryDirectory() as temporary_directory:
concatenate_protocol = ConcatenateTrajectories('concatenate_protocol')
concatenate_protocol.input_coordinate_paths = [coordinate_path, coordinate_path]
concatenate_protocol.input_trajectory_paths = [trajectory_path, trajectory_path]
result = concatenate_protocol.execute(temporary_directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
final_trajectory = mdtraj.load(concatenate_protocol.output_trajectory_path, top=coordinate_path)
assert len(final_trajectory) == len(original_trajectory) * 2
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 test_extract_uncorrelated_statistics_data():
statistics_path = get_data_filename('test/statistics/stats_pandas.csv')
original_array = StatisticsArray.from_pandas_csv(statistics_path)
with tempfile.TemporaryDirectory() as temporary_directory:
extract_protocol = ExtractUncorrelatedStatisticsData(
'extract_protocol')
extract_protocol.input_statistics_path = statistics_path
extract_protocol.equilibration_index = 2
extract_protocol.statistical_inefficiency = 2.0
result = extract_protocol.execute(temporary_directory,
ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
final_array = StatisticsArray.from_pandas_csv(
extract_protocol.output_statistics_path)
assert len(final_array) == (len(original_array) - 2) / 2
assert extract_protocol.number_of_uncorrelated_samples == (
len(original_array) - 2) / 2
def test_run_openmm_simulation():
thermodynamic_state = ThermodynamicState(298 * unit.kelvin,
1.0 * unit.atmosphere)
with tempfile.TemporaryDirectory() as directory:
coordinate_path, system_path = _setup_dummy_system(directory)
npt_equilibration = RunOpenMMSimulation('npt_equilibration')
npt_equilibration.steps_per_iteration = 2
npt_equilibration.output_frequency = 1
npt_equilibration.thermodynamic_state = thermodynamic_state
npt_equilibration.input_coordinate_file = coordinate_path
npt_equilibration.system_path = system_path
result = npt_equilibration.execute(directory, ComputeResources())
assert not isinstance(result, PropertyEstimatorException)
assert path.isfile(npt_equilibration.output_coordinate_file)
assert path.isfile(npt_equilibration.trajectory_file_path)
assert path.isfile(npt_equilibration.statistics_file_path)
def test_simple_workflow_graph():
dummy_schema = WorkflowSchema()
dummy_protocol_a = DummyInputOutputProtocol('protocol_a')
dummy_protocol_a.input_value = EstimatedQuantity(1 * unit.kelvin, 0.1 * unit.kelvin, 'dummy_source')
dummy_schema.protocols[dummy_protocol_a.id] = dummy_protocol_a.schema
dummy_protocol_b = DummyInputOutputProtocol('protocol_b')
dummy_protocol_b.input_value = ProtocolPath('output_value', dummy_protocol_a.id)
dummy_schema.protocols[dummy_protocol_b.id] = dummy_protocol_b.schema
dummy_schema.final_value_source = ProtocolPath('output_value', dummy_protocol_b.id)
dummy_schema.validate_interfaces()
dummy_property = create_dummy_property(Density)
dummy_workflow = Workflow(dummy_property, {})
dummy_workflow.schema = dummy_schema
with tempfile.TemporaryDirectory() as temporary_directory:
workflow_graph = WorkflowGraph(temporary_directory)
workflow_graph.add_workflow(dummy_workflow)
dask_local_backend = DaskLocalCluster(1, ComputeResources(1))
dask_local_backend.start()
results_futures = workflow_graph.submit(dask_local_backend)
assert len(results_futures) == 1
result = results_futures[0].result()
assert isinstance(result, CalculationLayerResult)
assert result.calculated_property.value == 1 * unit.kelvin
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 generate_trajectories():
"""Generates trajectories to subsample.
"""
setup_timestamp_logging()
logger = logging.getLogger()
substance = Substance.from_components('C(C(C(C(C(F)(F)Br)(F)F)(F)F)(F)F)(C(C(C(F)(F)F)(F)F)(F)F)(F)F')
logger.info('Building system.')
build_system = BuildSmirnoffSystem('build_system')
build_system.coordinate_file_path = 'coords.pdb'
build_system.substance = substance
build_system.force_field_path = 'smirnoff99Frosst-1.1.0.offxml'
build_system.execute('', None)
logger.info('System built.')
production_simulation = RunOpenMMSimulation(f'production_simulation')
production_simulation.steps_per_iteration = 500
production_simulation.output_frequency = 1
production_simulation.timestep = 2.0 * unit.femtosecond
production_simulation.thermodynamic_state = ThermodynamicState(temperature=298.15*unit.kelvin,
pressure=1.0*unit.atmosphere)
production_simulation.input_coordinate_file = 'coords.pdb'
production_simulation.system_path = 'system.xml'
compute_resources = ComputeResources(number_of_threads=4)
logger.info(f'Simulation started.')
production_simulation_schema = production_simulation.schema
production_simulation.execute('', compute_resources)
production_simulation.schema = production_simulation_schema
logger.info(f'Simulation finished.')
def test_estimate_request():
"""Test sending an estimator request to a server."""
from openforcefield.typing.engines import smirnoff
with tempfile.TemporaryDirectory() as temporary_directory:
storage_directory = path.join(temporary_directory, 'storage')
working_directory = path.join(temporary_directory, 'working')
dummy_property = create_dummy_property(Density)
dummy_data_set = PhysicalPropertyDataSet()
dummy_data_set.properties[dummy_property.substance.identifier] = [
dummy_property
]
force_field = smirnoff.ForceField(
get_data_filename('forcefield/smirnoff99Frosst.offxml'))
calculation_backend = DaskLocalClusterBackend(1, ComputeResources())
storage_backend = LocalFileStorage(storage_directory)
PropertyEstimatorServer(calculation_backend,
storage_backend,
working_directory=working_directory)
property_estimator = PropertyEstimatorClient()
options = PropertyEstimatorOptions(
allowed_calculation_layers=[TestCalculationLayer])
request = property_estimator.request_estimate(dummy_data_set,
force_field, options)
result = request.results(synchronous=True, polling_interval=0)
assert not isinstance(result, PropertyEstimatorException)
def test_build_docked_coordinates_protocol():
"""Tests docking a methanol molecule into alpha-Cyclodextrin."""
ligand_substance = Substance()
ligand_substance.add_component(
Substance.Component('CO', role=Substance.ComponentRole.Ligand),
Substance.ExactAmount(1))
# TODO: This test could likely be made substantially faster
# by storing the binary prepared receptor. Would this
# be in breach of any oe license terms?
with tempfile.TemporaryDirectory() as temporary_directory:
build_docked_coordinates = BuildDockedCoordinates('build_methanol')
build_docked_coordinates.ligand_substance = ligand_substance
build_docked_coordinates.number_of_ligand_conformers = 5
build_docked_coordinates.receptor_coordinate_file = get_data_filename(
'test/molecules/acd.mol2')
build_docked_coordinates.execute(temporary_directory,
ComputeResources())
docked_pdb = PDBFile(
build_docked_coordinates.docked_complex_coordinate_path)
assert docked_pdb.topology.getNumResidues() == 2
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)