GradientReducedPotentials

class propertyestimator.protocols.gradients.GradientReducedPotentials(protocol_id)[source]

A protocol to estimates the the reduced potential of the configurations of a trajectory using reverse and forward perturbed simulation parameters for use with estimating reweighted gradients using the central difference method.

__init__(protocol_id)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(protocol_id)

Initialize self.

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.

coordinate_file_path

Protocol Input - A path to a PDB coordinate file which describes the topology of the system.

dependencies

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

effective_sample_indices

Protocol Input - This a placeholder input which is not currently implemented.

enable_pbc

Protocol Input - If true, periodic boundary conditions will be enabled when re-evaluating the reduced potentials.

force_field_path

Protocol Input - The path to the force field which contains the parameters to differentiate the observable with respect to.

forward_parameter_value

Protocol Output - The value of the parameter perturbed in the forward direction.

forward_potentials_path

Protocol Output - A file path to the energies evaluated using the parametersperturbed in the forward direction.

id

The unique id of this protocol.

parameter_key

Protocol Input - The key of the parameter to differentiate with respect to.

perturbation_scale

Protocol Input - The amount to perturb the parameter by, such that p_new = p_old * (1 +/- perturbation_scale) The default value of this attribute is 0.0001.

reference_force_field_paths

Protocol Input - A list of paths to the force field files which were originally used to generate the configurations.

reference_potential_paths

Protocol Output - File paths to the reduced potentials evaluated using each of the reference force fields.

reference_statistics_path

Protocol Input - An optional path to the statistics array which was generated alongside the observable of interest, which will be used to correct the potential energies at the reverse and forward states.

reverse_parameter_value

Protocol Output - The value of the parameter perturbed in the reverse direction.

reverse_potentials_path

Protocol Output - A file path to the energies evaluated using the parametersperturbed in the reverse direction.

schema

A serializable schema for this object.

substance

Protocol Input - The substance which describes the composition of the system.

thermodynamic_state

Protocol Input - The thermodynamic state to estimate the gradients at.

trajectory_file_path

Protocol Input - A path to the trajectory of configurations The default value of this attribute is not set and must be set by the user..

use_subset_of_force_field

Protocol Input - If true, the reduced potential will be estimated using an OpenMM system which only contains the parameter of interest The default value of this attribute is True.

reference_force_field_paths

Protocol Input - A list of paths to the force field files which were originally used to generate the configurations. The default value of this attribute is not set and must be set by the user..

Type

list

force_field_path

Protocol Input - The path to the force field which contains the parameters to differentiate the observable with respect to. The default value of this attribute is not set and must be set by the user..

Type

str

reference_statistics_path

Protocol Input - An optional path to the statistics array which was generated alongside the observable of interest, which will be used to correct the potential energies at the reverse and forward states. This is only really needed when the observable of interest is an energy. The default value of this attribute is not set. This input is optional.

Type

str

enable_pbc

Protocol Input - If true, periodic boundary conditions will be enabled when re-evaluating the reduced potentials. The default value of this attribute is True.

Type

bool

substance

Protocol Input - The substance which describes the composition of the system. The default value of this attribute is not set and must be set by the user..

Type

Substance

thermodynamic_state

Protocol Input - The thermodynamic state to estimate the gradients at. The default value of this attribute is not set and must be set by the user..

Type

ThermodynamicState

coordinate_file_path

Protocol Input - A path to a PDB coordinate file which describes the topology of the system. The default value of this attribute is not set and must be set by the user..

Type

str

trajectory_file_path

Protocol Input - A path to the trajectory of configurations The default value of this attribute is not set and must be set by the user..

Type

str

parameter_key

Protocol Input - The key of the parameter to differentiate with respect to. The default value of this attribute is not set and must be set by the user..

Type

ParameterGradientKey

perturbation_scale

Protocol Input - The amount to perturb the parameter by, such that p_new = p_old * (1 +/- perturbation_scale) The default value of this attribute is 0.0001.

Type

float

use_subset_of_force_field

Protocol Input - If true, the reduced potential will be estimated using an OpenMM system which only contains the parameter of interest The default value of this attribute is True.

Type

bool

effective_sample_indices

Protocol Input - This a placeholder input which is not currently implemented. The default value of this attribute is not set. This input is optional.

Type

list

reference_potential_paths

Protocol Output - File paths to the reduced potentials evaluated using each of the reference force fields.

Type

list

reverse_potentials_path

Protocol Output - A file path to the energies evaluated using the parametersperturbed in the reverse direction.

Type

str

forward_potentials_path

Protocol Output - A file path to the energies evaluated using the parametersperturbed in the forward direction.

Type

str

reverse_parameter_value

Protocol Output - The value of the parameter perturbed in the reverse direction.

Type

Quantity

forward_parameter_value

Protocol Output - The value of the parameter perturbed in the forward direction.

Type

Quantity

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

property dependencies

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

Type

list of ProtocolPath

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]

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.