def _get_schema(self): """Returns the schema that describes this workflow. Returns ------- WorkflowSchema The schema that describes this workflow. """ schema = WorkflowSchema() schema.id = self.uuid schema.protocol_schemas = [ copy.deepcopy(x.schema) for x in self._protocols ] if self._final_value_source != UNDEFINED: schema.final_value_source = self._final_value_source.copy() schema.outputs_to_store = copy.deepcopy(self._outputs_to_store) return schema
def default_yank_schema(existing_schema=None): """Returns the default calculation schema to use when estimating this class of property from direct simulations. Parameters ---------- existing_schema: SimulationSchema, optional An existing schema whose settings to use. If set, the schema's `workflow_schema` will be overwritten by this method. Returns ------- SimulationSchema The schema to follow when estimating this property. """ calculation_schema = SimulationSchema() if existing_schema is not None: assert isinstance(existing_schema, SimulationSchema) calculation_schema = copy.deepcopy(existing_schema) schema = WorkflowSchema( property_type=HostGuestBindingAffinity.__name__) schema.id = "{}{}".format(HostGuestBindingAffinity.__name__, "Schema") # Initial coordinate and topology setup. filter_ligand = miscellaneous.FilterSubstanceByRole("filter_ligand") filter_ligand.input_substance = ProtocolPath("substance", "global") filter_ligand.component_roles = [Component.Role.Ligand] # We only support substances with a single guest ligand. filter_ligand.expected_components = 1 schema.protocols[filter_ligand.id] = filter_ligand.schema # Construct the protocols which will (for now) take as input a set of host coordinates, # and generate a set of charges for them. filter_receptor = miscellaneous.FilterSubstanceByRole( "filter_receptor") filter_receptor.input_substance = ProtocolPath("substance", "global") filter_receptor.component_roles = [Component.Role.Receptor] # We only support substances with a single host receptor. filter_receptor.expected_components = 1 schema.protocols[filter_receptor.id] = filter_receptor.schema # Perform docking to position the guest within the host. perform_docking = coordinates.BuildDockedCoordinates("perform_docking") perform_docking.ligand_substance = ProtocolPath( "filtered_substance", filter_ligand.id) perform_docking.receptor_coordinate_file = ProtocolPath( "receptor_mol2", "global") schema.protocols[perform_docking.id] = perform_docking.schema # Solvate the docked structure using packmol filter_solvent = miscellaneous.FilterSubstanceByRole("filter_solvent") filter_solvent.input_substance = ProtocolPath("substance", "global") filter_solvent.component_roles = [Component.Role.Solvent] schema.protocols[filter_solvent.id] = filter_solvent.schema solvate_complex = coordinates.SolvateExistingStructure( "solvate_complex") solvate_complex.max_molecules = 1000 solvate_complex.substance = ProtocolPath("filtered_substance", filter_solvent.id) solvate_complex.solute_coordinate_file = ProtocolPath( "docked_complex_coordinate_path", perform_docking.id) schema.protocols[solvate_complex.id] = solvate_complex.schema # Assign force field parameters to the solvated complex system. build_solvated_complex_system = forcefield.BaseBuildSystem( "build_solvated_complex_system") build_solvated_complex_system.force_field_path = ProtocolPath( "force_field_path", "global") build_solvated_complex_system.coordinate_file_path = ProtocolPath( "coordinate_file_path", solvate_complex.id) build_solvated_complex_system.substance = ProtocolPath( "substance", "global") build_solvated_complex_system.charged_molecule_paths = [ ProtocolPath("receptor_mol2", "global") ] schema.protocols[build_solvated_complex_system. id] = build_solvated_complex_system.schema # Solvate the ligand using packmol solvate_ligand = coordinates.SolvateExistingStructure("solvate_ligand") solvate_ligand.max_molecules = 1000 solvate_ligand.substance = ProtocolPath("filtered_substance", filter_solvent.id) solvate_ligand.solute_coordinate_file = ProtocolPath( "docked_ligand_coordinate_path", perform_docking.id) schema.protocols[solvate_ligand.id] = solvate_ligand.schema # Assign force field parameters to the solvated ligand system. build_solvated_ligand_system = forcefield.BaseBuildSystem( "build_solvated_ligand_system") build_solvated_ligand_system.force_field_path = ProtocolPath( "force_field_path", "global") build_solvated_ligand_system.coordinate_file_path = ProtocolPath( "coordinate_file_path", solvate_ligand.id) build_solvated_ligand_system.substance = ProtocolPath( "substance", "global") schema.protocols[build_solvated_ligand_system. id] = build_solvated_ligand_system.schema # Employ YANK to estimate the binding free energy. yank_protocol = yank.LigandReceptorYankProtocol("yank_protocol") yank_protocol.thermodynamic_state = ProtocolPath( "thermodynamic_state", "global") yank_protocol.number_of_iterations = 2000 yank_protocol.steps_per_iteration = 500 yank_protocol.checkpoint_interval = 10 yank_protocol.verbose = True yank_protocol.force_field_path = ProtocolPath("force_field_path", "global") yank_protocol.ligand_residue_name = ProtocolPath( "ligand_residue_name", perform_docking.id) yank_protocol.receptor_residue_name = ProtocolPath( "receptor_residue_name", perform_docking.id) yank_protocol.solvated_ligand_coordinates = ProtocolPath( "coordinate_file_path", solvate_ligand.id) yank_protocol.solvated_ligand_system = ProtocolPath( "parameterized_system", build_solvated_ligand_system.id) yank_protocol.solvated_complex_coordinates = ProtocolPath( "coordinate_file_path", solvate_complex.id) yank_protocol.solvated_complex_system = ProtocolPath( "parameterized_system", build_solvated_complex_system.id) schema.protocols[yank_protocol.id] = yank_protocol.schema # Define where the final values come from. schema.final_value_source = ProtocolPath("free_energy_difference", yank_protocol.id) calculation_schema.workflow_schema = schema return calculation_schema