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

A base class for protocols which will evaluate the reduced potentials of a series of configurations using a set of force field parameters which have been slightly increased and slightly decreased. These are mainly useful when estimating gradients with respect to force field parameters 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. from_json(file_path) Create this object from a JSON file. from_schema(schema) Initializes a protocol from it’s schema definition. get_attributes([attribute_type]) Returns all attributes of a specific attribute_type. 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. json([file_path, format]) Creates a JSON representation of this class. merge(other) Merges another Protocol with this one. parse_json(string_contents[, encoding]) Parses a typed json string into the corresponding class structure. replace_protocol(old_id, new_id) Finds each input which came from a given protocol set_uuid(value) Prepend a unique identifier to this protocols id. set_value(reference_path, value) Sets the value of one of this protocols inputs. validate([attribute_type]) Validate the values of the attributes.

Attributes

 allow_merging Input - Defines whether this protocols is allowed to merge with other protocols. coordinate_file_path 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 Input - This a placeholder input which is not currently implemented. enable_pbc Input - If true, periodic boundary conditions will be enabled when re-evaluating the reduced potentials. force_field_path Input - The path to the force field which contains the parameters to differentiate the observable with respect to. forward_parameter_value Output - The value of the parameter perturbed in the forward direction. forward_potentials_path Output - A file path to the energies evaluated using the parametersperturbed in the forward direction. id The unique id of this protocol. outputs A dictionary of the outputs of this property. parameter_key Input - The key of the parameter to differentiate with respect to. perturbation_scale 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. required_inputs The inputs which must be set on this protocol. reverse_parameter_value Output - The value of the parameter perturbed in the reverse direction. reverse_potentials_path Output - A file path to the energies evaluated using the parametersperturbed in the reverse direction. schema A serializable schema for this object. statistics_path 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 Input - The substance which describes the composition of the system. thermodynamic_state Input - The thermodynamic state to estimate the gradients at. trajectory_file_path 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 Input - If true, the reduced potentials will be estimated using a system which only contains the parameters of interest, e.g.
force_field_path

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

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

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

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

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

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

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

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

perturbation_scale

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

Input - If true, the reduced potentials will be estimated using a system which only contains the parameters of interest, e.g. if the gradient of interest is with respect to the VdW epsilon parameter, then all valence / electrostatic terms will be ignored. The default value of this attribute is True.

Type

bool

effective_sample_indices

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

Type

list

reverse_potentials_path

Output - A file path to the energies evaluated using the parametersperturbed in the reverse direction. The default value of this attribute is not set and must be set by the user..

Type

str

forward_potentials_path

Output - A file path to the energies evaluated using the parametersperturbed in the forward direction. The default value of this attribute is not set and must be set by the user..

Type

str

reverse_parameter_value

Output - The value of the parameter perturbed in the reverse direction. The default value of this attribute is not set and must be set by the user..

Type

Quantity

forward_parameter_value

Output - The value of the parameter perturbed in the forward direction. The default value of this attribute is not set and must be set by the user..

Type

Quantity

allow_merging

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 (Protocol) – 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

execute(directory='', available_resources=None)

Execute the protocol.

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

• available_resources (ComputeResources) – The resources available to execute on. If None, the protocol will be executed on a single CPU.

classmethod from_json(file_path)

Create this object from a JSON file.

Parameters

file_path (str) – The path to load the JSON from.

Returns

The parsed class.

Return type

cls

classmethod from_schema(schema)

Initializes a protocol from it’s schema definition.

Parameters

schema (ProtocolSchema) – The schema to initialize the protocol using.

Returns

The initialized protocol.

Return type

cls

classmethod get_attributes(attribute_type=None)

Returns all attributes of a specific attribute_type.

Parameters

attribute_type (type of Attribute, optional) – The type of attribute to search for.

Returns

The names of the attributes of the specified type.

Return type

list of str

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

id

The unique id of this protocol. The default value of this attribute is not set and must be set by the user..

Type

str

json(file_path=None, format=False)

Creates a JSON representation of this class.

Parameters
• file_path (str, optional) – The (optional) file path to save the JSON file to.

• format (bool) – Whether to format the JSON or not.

Returns

The JSON representation of this class.

Return type

str

merge(other)

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

Parameters

other (Protocol) – 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]

property outputs

A dictionary of the outputs of this property.

Type

dict of ProtocolPath and Any

classmethod parse_json(string_contents, encoding='utf8')

Parses a typed json string into the corresponding class structure.

Parameters
• string_contents (str or bytes) – The typed json string.

• encoding (str) – The encoding of the string_contents.

Returns

The parsed class.

Return type

Any

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 required_inputs

The inputs which must be set on this protocol.

Type

list of ProtocolPath

property schema

A serializable schema for this object.

Type

ProtocolSchema

set_uuid(value)

Prepend a unique identifier to this protocols id. If the id already has a prepended uuid, it will be overwritten by this value.

Parameters

value (str) – The uuid to prepend.

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.

validate(attribute_type=None)

Validate the values of the attributes. If attribute_type is set, only attributes of that type will be validated.

Parameters

attribute_type (type of Attribute, optional) – The type of attribute to validate.

Raises