LigandReceptorYankProtocol

class propertyestimator.protocols.yank.LigandReceptorYankProtocol(protocol_id)[source]

A protocol for performing ligand-receptor alchemical free energy calculations using the YANK framework.

__init__(protocol_id)[source]

Constructs a new LigandReceptorYankProtocol object.

Methods

__init__(protocol_id)

Constructs a new LigandReceptorYankProtocol object.

apply_replicator(replicator, template_values)

Applies a ProtocolReplicator to this protocol.

can_merge(other[, path_replacements])

Determines whether this protocol can be merged with another.

execute(directory, available_resources)

Execute the protocol.

get_class_attribute(reference_path)

Returns one of this protocols, or any of its children’s, attributes directly (rather than its value).

get_value(reference_path)

Returns the value of one of this protocols inputs / outputs.

get_value_references(input_path)

Returns a dictionary of references to the protocols which one of this protocols inputs (specified by input_path) takes its value from.

merge(other)

Merges another BaseProtocol with this one.

replace_protocol(old_id, new_id)

Finds each input which came from a given protocol

set_uuid(value)

Store the uuid of the calculation this protocol belongs to

set_value(reference_path, value)

Sets the value of one of this protocols inputs.

Attributes

allow_merging

Protocol Input - Defines whether this protocols is allowed to merge with other protocols.

apply_restraints

Protocol Input - Determines whether the ligand should be explicitly restrained to the receptor in order to stop the ligand from temporarily unbinding.

checkpoint_interval

Protocol Input - The number of iterations between saving YANK checkpoint files.

dependencies

A list of pointers to the protocols which this protocol takes input from.

estimated_free_energy

Protocol Output - The estimated free energy value and its uncertainty returned by YANK.

force_field_path

Protocol Input - The path to the force field which defines the charge method to use for the calculation.

id

The unique id of this protocol.

ligand_residue_name

Protocol Input - The residue name of the ligand.

number_of_equilibration_iterations

Protocol Input - The number of iterations used for equilibration before production run.

number_of_iterations

Protocol Input - The number of YANK iterations to perform.

receptor_residue_name

Protocol Input - The residue name of the receptor.

restraint_type

Protocol Input - The type of ligand restraint applied, provided that apply_restraints is True The default value of this attribute is RestraintType.Harmonic.

schema

A serializable schema for this object.

setup_only

Protocol Input - If true, YANK will only create and validate the setup files, but not actually run any simulations.

solvated_complex_coordinates

Protocol Input - The file path to the solvated complex coordinates.

solvated_complex_system

Protocol Input - The file path to the solvated complex system object.

solvated_complex_trajectory_path

Protocol Output - The file path to the generated ligand trajectory.

solvated_ligand_coordinates

Protocol Input - The file path to the solvated ligand coordinates.

solvated_ligand_system

Protocol Input - The file path to the solvated ligand system object.

solvated_ligand_trajectory_path

Protocol Output - The file path to the generated ligand trajectory.

steps_per_iteration

Protocol Input - The number of steps per YANK iteration to perform.

thermodynamic_state

Protocol Input - The state at which to run the calculations.

timestep

Protocol Input - The length of the timestep to take.

verbose

Protocol Input - Controls whether or not to run YANK at high verbosity.

class RestraintType[source]

The types of ligand restraints available within yank.

ligand_residue_name

Protocol Input - The residue name of the ligand. The default value of this attribute is not set and must be set by the user..

Type

str

receptor_residue_name

Protocol Input - The residue name of the receptor. The default value of this attribute is not set and must be set by the user..

Type

str

solvated_ligand_coordinates

Protocol Input - The file path to the solvated ligand coordinates. The default value of this attribute is not set and must be set by the user..

Type

str

solvated_ligand_system

Protocol Input - The file path to the solvated ligand system object. The default value of this attribute is not set and must be set by the user..

Type

str

solvated_complex_coordinates

Protocol Input - The file path to the solvated complex coordinates. The default value of this attribute is not set and must be set by the user..

Type

str

solvated_complex_system

Protocol Input - The file path to the solvated complex system object. The default value of this attribute is not set and must be set by the user..

Type

str

force_field_path

Protocol Input - The path to the force field which defines the charge method to use for the calculation. The default value of this attribute is not set and must be set by the user..

Type

str

apply_restraints

Protocol Input - Determines whether the ligand should be explicitly restrained to the receptor in order to stop the ligand from temporarily unbinding. The default value of this attribute is True.

Type

bool

restraint_type

Protocol Input - The type of ligand restraint applied, provided that apply_restraints is True The default value of this attribute is RestraintType.Harmonic.

Type

LigandReceptorYankProtocol.RestraintType

solvated_ligand_trajectory_path

Protocol Output - The file path to the generated ligand trajectory.

Type

str

solvated_complex_trajectory_path

Protocol Output - The file path to the generated ligand trajectory.

Type

str

execute(directory, available_resources)[source]

Execute the protocol.

Protocols may be chained together by passing the output of previous protocols as input to the current one.

Parameters
  • directory (str) – The directory to store output data in.

  • available_resources (ComputeResources) – The resources available to execute on.

Returns

The output of the execution.

Return type

Dict[str, Any]

allow_merging

Protocol Input - Defines whether this protocols is allowed to merge with other protocols. The default value of this attribute is True.

Type

bool

apply_replicator(replicator, template_values, template_index=-1, template_value=None, update_input_references=False)

Applies a ProtocolReplicator to this protocol. This method should clone any protocols whose id contains the id of the replicator (in the format $(replicator.id)).

Parameters
  • replicator (ProtocolReplicator) – The replicator to apply.

  • template_values (list of Any) –

    A list of the values which will be inserted into the newly replicated protocols.

    This parameter is mutually exclusive with template_index and template_value

  • template_index (int, optional) –

    A specific value which should be used for any protocols flagged as to be replicated by the replicator. This option is mainly used when replicating children of an already replicated protocol.

    This parameter is mutually exclusive with template_values and must be set along with a template_value.

  • template_value (Any, optional) –

    A specific index which should be used for any protocols flagged as to be replicated by the replicator. This option is mainly used when replicating children of an already replicated protocol.

    This parameter is mutually exclusive with template_values and must be set along with a template_index.

  • update_input_references (bool) –

    If true, any protocols which take their input from a protocol which was flagged for replication will be updated to take input from the actually replicated protocol. This should only be set to true if this protocol is not nested within a workflow or a protocol group.

    This option cannot be used when a specific template_index or template_value is providied.

Returns

A dictionary of references to all of the protocols which have been replicated, with keys of original protocol ids. Each value is comprised of a list of the replicated protocol ids, and their index into the template_values array.

Return type

dict of ProtocolPath and list of tuple of ProtocolPath and int

can_merge(other, path_replacements=None)

Determines whether this protocol can be merged with another.

Parameters
  • other (BaseProtocol) – The protocol to compare against.

  • path_replacements (list of tuple of str, optional) – Replacements to make in any value reference protocol paths before comparing for equality.

Returns

True if the two protocols are safe to merge.

Return type

bool

checkpoint_interval

Protocol Input - The number of iterations between saving YANK checkpoint files. The default value of this attribute is 50. When two protocols are merged, the largest value of this attribute from either protocol is retained.

Type

int

property dependencies

A list of pointers to the protocols which this protocol takes input from.

Type

list of ProtocolPath

estimated_free_energy

Protocol Output - The estimated free energy value and its uncertainty returned by YANK.

Type

EstimatedQuantity

get_class_attribute(reference_path)

Returns one of this protocols, or any of its children’s, attributes directly (rather than its value).

Parameters

reference_path (ProtocolPath) – The path pointing to the attribute to return.

Returns

The class attribute.

Return type

object

get_value(reference_path)

Returns the value of one of this protocols inputs / outputs.

Parameters

reference_path (ProtocolPath) – The path pointing to the value to return.

Returns

The value of the input / output

Return type

Any

get_value_references(input_path)

Returns a dictionary of references to the protocols which one of this protocols inputs (specified by input_path) takes its value from.

Notes

Currently this method only functions correctly for an input value which is either currently a ProtocolPath, or a list / dict which contains at least one ProtocolPath.

Parameters

input_path (propertyestimator.workflow.utils.ProtocolPath) – The input value to check.

Returns

A dictionary of the protocol paths that the input targeted by input_path depends upon.

Return type

dict of ProtocolPath and ProtocolPath

property id

The unique id of this protocol.

Type

str

merge(other)

Merges another BaseProtocol with this one. The id of this protocol will remain unchanged.

It is assumed that can_merge has already returned that these protocols are compatible to be merged together.

Parameters

other (BaseProtocol) – The protocol to merge into this one.

Returns

A map between any original protocol ids and their new merged values.

Return type

Dict[str, str]

number_of_equilibration_iterations

Protocol Input - The number of iterations used for equilibration before production run. Only post-equilibration iterations are written to file. The default value of this attribute is 1.

Type

int

number_of_iterations

Protocol Input - The number of YANK iterations to perform. The default value of this attribute is 5000.

Type

int

replace_protocol(old_id, new_id)
Finds each input which came from a given protocol

and redirects it to instead take input from a new one.

Notes

This method is mainly intended to be used only when merging multiple protocols into one.

Parameters
  • old_id (str) – The id of the old input protocol.

  • new_id (str) – The id of the new input protocol.

property schema

A serializable schema for this object.

Type

ProtocolSchema

set_uuid(value)

Store the uuid of the calculation this protocol belongs to

Parameters

value (str) – The uuid of the parent calculation.

set_value(reference_path, value)

Sets the value of one of this protocols inputs.

Parameters
  • reference_path (ProtocolPath) – The path pointing to the value to return.

  • value (Any) – The value to set.

setup_only

Protocol Input - If true, YANK will only create and validate the setup files, but not actually run any simulations. This argument is mainly only to be used for testing purposes. The default value of this attribute is False.

Type

bool

steps_per_iteration

Protocol Input - The number of steps per YANK iteration to perform. The default value of this attribute is 500.

Type

int

thermodynamic_state

Protocol Input - The state at which to run the calculations. The default value of this attribute is not set and must be set by the user..

Type

ThermodynamicState

timestep

Protocol Input - The length of the timestep to take. The default value of this attribute is 2 femtosecond. When two protocols are merged, the largest value of this attribute from either protocol is retained.

Type

Quantity

verbose

Protocol Input - Controls whether or not to run YANK at high verbosity. The default value of this attribute is False.

Type

bool