BaseMBARProtocol

class propertyestimator.protocols.reweighting.BaseMBARProtocol(protocol_id)[source]

Reweights a set of observables using MBAR to calculate the average value of the observables at a different state than they were originally measured.

__init__(protocol_id)[source]

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.

bootstrap_iterations

Input - The number of bootstrap iterations to perform if bootstraped uncertainties have been requested The default value of this attribute is 1.

bootstrap_sample_size

Input - The relative bootstrap sample size to use if bootstraped uncertainties have been requested The default value of this attribute is 1.0.

bootstrap_uncertainties

Input - If true, bootstrapping will be used to estimated the total uncertainty The default value of this attribute is False.

dependencies

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

effective_sample_indices

Output - The indices of those samples which have a non-zero weight.

effective_samples

Output - The number of effective samples which were reweighted.

id

The unique id of this protocol.

outputs

A dictionary of the outputs of this property.

reference_reduced_potentials

Input - A list of paths to the reduced potentials of each reference state.

required_effective_samples

Input - The minimum number of MBAR effective samples for the reweighted value to be trusted.

required_inputs

The inputs which must be set on this protocol.

schema

A serializable schema for this object.

target_reduced_potentials

Input - A list of paths to the reduced potentials of the target state.

value

Output - The reweighted average value of the observable at the target state.

reference_reduced_potentials

Input - A list of paths to the reduced potentials of each reference state. The default value of this attribute is not set and must be set by the user..

Type

typing.Union[str, list]

target_reduced_potentials

Input - A list of paths to the reduced potentials of the target state. The default value of this attribute is not set and must be set by the user..

Type

typing.Union[str, list]

bootstrap_uncertainties

Input - If true, bootstrapping will be used to estimated the total uncertainty The default value of this attribute is False.

Type

bool

bootstrap_iterations

Input - The number of bootstrap iterations to perform if bootstraped uncertainties have been requested The default value of this attribute is 1.

Type

int

bootstrap_sample_size

Input - The relative bootstrap sample size to use if bootstraped uncertainties have been requested The default value of this attribute is 1.0.

Type

float

required_effective_samples

Input - The minimum number of MBAR effective samples for the reweighted value to be trusted. If this minimum is not met then the uncertainty will be set to sys.float_info.max The default value of this attribute is 50.

Type

int

value

Output - The reweighted average value of the observable at the target state. The default value of this attribute is not set and must be set by the user..

Type

Measurement

effective_samples

Output - The number of effective samples which were reweighted. The default value of this attribute is not set and must be set by the user..

Type

float

effective_sample_indices

Output - The indices of those samples which have a non-zero weight. The default value of this attribute is not set and must be set by the user..

Type

list

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

ValueError or AssertionError