total_free_energy.thermodynamic_state = ProtocolPath(
"thermodynamic_state", "global")
calculation_schema.workflow_schema = WorkflowSchema()
calculation_schema.workflow_schema.protocol_schemas = [
*(protocol.schema for protocol in attach_pull_protocols),
*(protocol.schema for protocol in release_protocols),
symmetry_correction.schema,
orientation_free_energy.schema,
total_free_energy.schema,
]
calculation_schema.workflow_schema.protocol_replicators = [
orientation_replicator,
*attach_pull_replicators,
release_replicator,
]
# Define where the final value comes from.
calculation_schema.workflow_schema.final_value_source = ProtocolPath(
"result", total_free_energy.id)
return calculation_schema
register_calculation_schema(
HostGuestBindingAffinity,
SimulationLayer,
HostGuestBindingAffinity.default_paprika_schema,
)
total_iterations.id)
conditional_group.add_protocols(total_iterations, run_yank)
# Define the full workflow schema.
schema = WorkflowSchema()
schema.protocol_schemas = [
build_full_coordinates.schema,
assign_full_parameters.schema,
energy_minimisation.schema,
equilibration_simulation.schema,
filter_solvent.schema,
filter_solute.schema,
build_vacuum_coordinates.schema,
assign_vacuum_parameters.schema,
conditional_group.schema,
]
schema.final_value_source = ProtocolPath("estimated_free_energy",
conditional_group.id,
run_yank.id)
calculation_schema.workflow_schema = schema
return calculation_schema
# Register the properties via the plugin system.
register_calculation_schema(SolvationFreeEnergy, SimulationLayer,
SolvationFreeEnergy.default_simulation_schema)
schema.protocol_replicators = [
full_data_replicator,
component_replicator,
component_data_replicator,
gradient_replicator,
]
schema.gradients_sources = [ProtocolPath("result", combine_gradients.id)]
schema.final_value_source = ProtocolPath("result", calculate_excess_volume.id)
calculation_schema.workflow_schema = schema
return calculation_schema
# Register the properties via the plugin system.
register_calculation_schema(Density, SimulationLayer, Density.default_simulation_schema)
register_calculation_schema(
Density, ReweightingLayer, Density.default_reweighting_schema
)
register_calculation_schema(
ExcessMolarVolume,
SimulationLayer,
ExcessMolarVolume.default_simulation_schema,
)
register_calculation_schema(
ExcessMolarVolume,
ReweightingLayer,
ExcessMolarVolume.default_reweighting_schema,
)
*(x.schema for x in gas_protocols if x is not None),
divide_by_liquid_molecules.schema,
energy_of_vaporization.schema,
ideal_volume.schema,
enthalpy_of_vaporization.schema,
]
schema.protocol_replicators = [liquid_replicator, gas_replicator]
schema.final_value_source = ProtocolPath("result", enthalpy_of_vaporization.id)
calculation_schema.workflow_schema = schema
return calculation_schema
# Register the properties via the plugin system.
register_calculation_schema(
EnthalpyOfMixing, SimulationLayer, EnthalpyOfMixing.default_simulation_schema
)
register_calculation_schema(
EnthalpyOfMixing, ReweightingLayer, EnthalpyOfMixing.default_reweighting_schema
)
register_calculation_schema(
EnthalpyOfVaporization,
SimulationLayer,
EnthalpyOfVaporization.default_simulation_schema,
)
register_calculation_schema(
EnthalpyOfVaporization,
ReweightingLayer,
EnthalpyOfVaporization.default_reweighting_schema,
)
protocols.reweight_observable.volumes = ProtocolPath(
"output_observables", protocols.decorrelate_observable.id
)
protocols.reweight_observable.thermodynamic_state = ProtocolPath(
"thermodynamic_state", "global"
)
schema = WorkflowSchema()
schema.protocol_schemas = [
*(x.schema for x in protocols),
compute_dipoles.schema,
join_dipoles.schema,
decorrelate_dipoles.schema,
]
schema.protocol_replicators = [data_replicator]
schema.final_value_source = ProtocolPath(
"value", protocols.reweight_observable.id
)
calculation_schema.workflow_schema = schema
return calculation_schema
# Register the properties via the plugin system.
register_calculation_schema(
DielectricConstant, SimulationLayer, DielectricConstant.default_simulation_schema
)
register_calculation_schema(
DielectricConstant, ReweightingLayer, DielectricConstant.default_reweighting_schema
)