StoredSimulationData

class openff.evaluator.storage.data.StoredSimulationData[source]

A representation of data which has been cached from a single previous simulation.

Notes

The ancillary directory which stores larger information such as trajectories should be of the form:

|--- data_object.json
|--- data_directory
     |--- coordinate_file_name.pdb
     |--- trajectory_file_name.dcd
__init__()

Methods

__init__()

from_json(file_path)

Create this object from a JSON file.

get_attributes([attribute_type])

Returns all attributes of a specific attribute_type.

has_ancillary_data()

Returns whether this data object requires an accompanying data directory-like structure.

json([file_path, format])

Creates a JSON representation of this class.

most_information(stored_data_1, stored_data_2)

Returns the data object with the lowest statistical_inefficiency.

parse_json(string_contents)

Parses a typed json string into the corresponding class structure.

to_storage_query()

returns

The storage query which would match this

validate([attribute_type])

Validate the values of the attributes.

Attributes

coordinate_file_name

The name of a coordinate file which encodes the topology information of the system.

force_field_id

The id of the force field parameters used to generate the data.

number_of_molecules

The total number of molecules in the system.

observables

A frame of observables collected over the duration of the simulation.

property_phase

The phase of the system (e.g.

source_calculation_id

The server id of the calculation which yielded this data.

statistical_inefficiency

The statistical inefficiency of the collected data.

substance

A description of the composition of the stored system.

thermodynamic_state

The state at which the data was collected.

trajectory_file_name

The name of a .dcd trajectory file containing configurations generated by the simulation.

coordinate_file_name

The name of a coordinate file which encodes the topology information of the system. The default value of this attribute is not set and must be set by the user..

Type

FilePath

trajectory_file_name

The name of a .dcd trajectory file containing configurations generated by the simulation. The default value of this attribute is not set and must be set by the user..

Type

FilePath

observables

A frame of observables collected over the duration of the simulation. The default value of this attribute is not set and must be set by the user..

Type

ObservableFrame

statistical_inefficiency

The statistical inefficiency of the collected data. The default value of this attribute is not set and must be set by the user..

Type

float

number_of_molecules

The total number of molecules in the system. The default value of this attribute is not set and must be set by the user..

Type

int

classmethod most_information(stored_data_1, stored_data_2)[source]

Returns the data object with the lowest statistical_inefficiency.

Parameters
Return type

StoredSimulationData

to_storage_query()[source]
Returns

The storage query which would match this data object.

Return type

SimulationDataQuery

force_field_id

The id of the force field parameters used to generate the data. The default value of this attribute is not set and must be set by the user..

Type

str

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 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

classmethod has_ancillary_data()

Returns whether this data object requires an accompanying data directory-like structure.

Returns

True if this class requires an accompanying data directory-like structure.

Return type

bool

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

classmethod parse_json(string_contents)

Parses a typed json string into the corresponding class structure.

Parameters

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

Returns

The parsed class.

Return type

Any

property_phase

The phase of the system (e.g. liquid, gas). The default value of this attribute is not set and must be set by the user..

Type

PropertyPhase

source_calculation_id

The server id of the calculation which yielded this data. The default value of this attribute is not set and must be set by the user..

Type

str

substance

A description of the composition of the stored system. The default value of this attribute is not set and must be set by the user..

Type

Substance

thermodynamic_state

The state at which the data was collected. The default value of this attribute is not set and must be set by the user..

Type

ThermodynamicState

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