Source code for propertyestimator.properties.binding

"""
A collection of density physical property definitions.
"""

from propertyestimator.properties import PhysicalProperty
from propertyestimator.properties.plugins import register_estimable_property
from propertyestimator.protocols import coordinates, forcefield, simulation, miscellaneous
from propertyestimator.substances import Substance
from propertyestimator.workflow.schemas import WorkflowSchema
from propertyestimator.workflow.utils import ProtocolPath


[docs]@register_estimable_property() class HostGuestBindingAffinity(PhysicalProperty): """A class representation of a host-guest binding affinity property""" @property def multi_component_property(self): """Returns whether this property is dependant on properties of the full mixed substance, or whether it is also dependant on the properties of the individual components also. """ return False
[docs] @staticmethod def get_default_workflow_schema(calculation_layer, options=None): if calculation_layer == 'SimulationLayer': return HostGuestBindingAffinity.get_default_simulation_workflow_schema(options) return None
[docs] @staticmethod def get_default_simulation_workflow_schema(options=None): """Returns the default workflow to use when estimating this property from direct simulations. Parameters ---------- options: WorkflowOptions The default options to use when setting up the estimation workflow. Returns ------- WorkflowSchema The schema to follow when estimating this property. """ 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_role = Substance.ComponentRole.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_role = Substance.ComponentRole.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_role = Substance.ComponentRole.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.BuildSmirnoffSystem('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.BuildSmirnoffSystem('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 = simulation.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('system_path', build_solvated_ligand_system.id) yank_protocol.solvated_complex_coordinates = ProtocolPath('coordinate_file_path', solvate_complex.id) yank_protocol.solvated_complex_system = ProtocolPath('system_path', 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('estimated_free_energy', yank_protocol.id) # output_to_store = WorkflowOutputToStore() # # output_to_store.trajectory_file_path = ProtocolPath('output_trajectory_path', # extract_uncorrelated_trajectory.id) # output_to_store.coordinate_file_path = ProtocolPath('output_coordinate_file', # converge_uncertainty.id, npt_production.id) # # output_to_store.statistics_file_path = ProtocolPath('output_statistics_path', # extract_uncorrelated_statistics.id) # # output_to_store.statistical_inefficiency = ProtocolPath('statistical_inefficiency', converge_uncertainty.id, # extract_density.id) # # schema.outputs_to_store = {'full_system': output_to_store} return schema