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__()¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`()	Initialize self.
`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[, encoding])	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

stored_data_1 (StoredSimulationData) – The first piece of data to compare.
stored_data_2 (StoredSimulationData) – The second piece of data to compare.

Returns

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, 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

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 –