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`.
`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.
`statistics_path`	Protocol Input - The path to a statistics array containing potentials evaluated at each frame of the trajectory using the input force_field_path and at the input thermodynamic_state.
`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 potentials will be estimated using an OpenMM system which only contains the parameters of interest The default value of this attribute is `True`.

force_field_path¶

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

Type: str

statistics_path¶

Protocol Input - The path to a statistics array containing potentials evaluated at each frame of the trajectory using the input force_field_path and at the input thermodynamic_state. The default value of this attribute is not set and must be set by the user..

Type: str

thermodynamic_state¶

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

Type: ThermodynamicState

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

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

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

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 potentials will be estimated using an OpenMM system which only contains the parameters 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

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.