def test_create_dataset(factory_dataset_type):
"""
Test making a the correct corresponding dataset type from a given factory type.
"""
factory = factory_dataset_type[0]()
element_filter = workflow_components.ElementFilter()
element_filter.allowed_elements = [1, 6, 8, 7]
factory.add_workflow_component(element_filter)
conformer_generator = workflow_components.StandardConformerGenerator(max_conformers=1)
factory.add_workflow_component(conformer_generator)
mols = Molecule.from_file(get_data("tautomers_small.smi"), "smi", allow_undefined_stereo=True)
# set some settings
changed_attrs = {"compute_tag": "test tag",
"dataset_tags": ["openff", "test"],
"maxiter": 400}
for attr, value in changed_attrs.items():
setattr(factory, attr, value)
dataset = factory.create_dataset(dataset_name="test name", molecules=mols, description="Force field test", tagline="A test dataset")
# check the attributes were changed
for attr, value in changed_attrs.items():
assert getattr(dataset, attr) == value
assert dataset.dataset_name == "test name"
assert isinstance(dataset, factory_dataset_type[1]) is True
# make sure molecules we filtered and passed
assert dataset.dataset != {}
assert dataset.filtered != {}
assert element_filter.component_name in dataset.filtered_molecules
def test_adding_workflow_components(factory_type):
"""
Test building workflows from a verity of workflow components.
"""
factory = factory_type()
# element filter
efilter = workflow_components.ElementFilter()
factory.add_workflow_component(efilter)
assert len(factory.workflow) == 1
# conformer generator
conformer_gen = workflow_components.StandardConformerGenerator()
conformer_gen.max_conformers = 200
factory.add_workflow_component(conformer_gen)
assert len(factory.workflow) == 2
# add element filter again and make sure the component name has been incremented
factory.add_workflow_component(efilter)
assert len(factory.workflow) == 3
assert efilter.component_name in factory.workflow
# try to add a non component
with pytest.raises(InvalidWorkflowComponentError):
factory.add_workflow_component(3)
with pytest.raises(ValidationError):
factory.workflow = {"first component": 3}
factory.workflow = {"test_conformer": conformer_gen}
assert len(factory.workflow) == 1
def test_element_filter_validators():
"""
Make sure the element filter validators are working.
"""
elem_filter = workflow_components.ElementFilter()
with pytest.raises(ValidationError):
elem_filter.allowed_elements = ["carbon", "hydrogen"]
elem_filter.allowed_elements = [1.02, 2.02, 3.03]
assert elem_filter.allowed_elements == [1, 2, 3]
assert "openmm_elements" in elem_filter.provenance(GLOBAL_TOOLKIT_REGISTRY)
def test_factory_round_trip(file_type, tmpdir):
"""
Test round tripping a factory to file with a workflow.
"""
with tmpdir.as_cwd():
factory = BasicDatasetFactory(driver="energy", maxiter=1)
efilter = workflow_components.ElementFilter()
weight = workflow_components.MolecularWeightFilter()
conformer = workflow_components.StandardConformerGenerator()
factory.add_workflow_components(efilter, weight, conformer)
file_name = "test." + file_type
factory.export(file_name)
factory2 = BasicDatasetFactory.from_file(file_name)
assert factory2.driver == factory.driver
assert factory2.workflow == factory.workflow
def test_get_wrokflow_component(factory_type):
"""
Test retrieving a workflow component.
"""
factory = factory_type()
efilter = workflow_components.ElementFilter()
weight = workflow_components.MolecularWeightFilter()
conformer = workflow_components.StandardConformerGenerator()
components = [efilter, weight, conformer]
factory.add_workflow_component(components)
for component in components:
assert factory.get_workflow_component(component.component_name) == component
def test_adding_multipule_workflow_components(factory_type):
"""
Test adding a list of workflow components.
"""
factory = factory_type()
efilter = workflow_components.ElementFilter()
weight = workflow_components.MolecularWeightFilter()
conformer = workflow_components.StandardConformerGenerator()
components = [efilter, weight, conformer]
factory.add_workflow_component(components)
assert len(factory.workflow) == 3
for component in components:
assert component.component_name in factory.workflow
def test_remove_workflow_componet(factory_type):
"""
Test removing a workflow component through the API.
"""
factory = factory_type()
efilter = workflow_components.ElementFilter()
weight = workflow_components.MolecularWeightFilter()
conformer = workflow_components.StandardConformerGenerator()
components = [efilter, weight, conformer]
factory.add_workflow_component(components)
assert len(factory.workflow) == 3
for component in components:
factory.remove_workflow_component(component.component_name)
assert factory.workflow == {}
def test_elementfilter_apply():
"""
Test applying the element filter to a workflow.
"""
elem_filter = workflow_components.ElementFilter()
elem_filter.allowed_elements = [1, 6, 7, 8]
mols = get_tautomers()
result = elem_filter.apply(mols, processors=1)
assert result.component_name == elem_filter.component_name
assert result.component_description == elem_filter.dict()
# make sure there are no unwanted elements in the pass set
for molecue in result.molecules:
for atom in molecue.atoms:
assert atom.atomic_number in elem_filter.allowed_elements
for molecue in result.filtered:
elements = set([atom.atomic_number for atom in molecue.atoms])
assert sorted(elements) != sorted(elem_filter.allowed_elements)
def test_clear_workflow(factory_type):
"""
Test clearing out the workflow.
"""
factory = factory_type()
efilter = workflow_components.ElementFilter()
weight = workflow_components.MolecularWeightFilter()
conformer = workflow_components.StandardConformerGenerator()
components = [efilter, weight, conformer]
factory.add_workflow_component(components)
factory.clear_workflow()
assert factory.workflow == {}
factory.add_workflow_component(components)
factory.workflow = {}
assert factory.workflow == {}
