StoredFreeEnergyData

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

A representation of data which has been cached from an free energy calculation which computed the free energy difference between a start and end state.

Notes

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

|--- data_object.json
|--- data_directory
     |--- topology_file_name.pdb
     |--- start_state_trajectory.dcd
     |--- end_state_trajectory.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)	A comparison function which will always retain both pieces of free energy data.
`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 data object.
`validate`([attribute_type])	Validate the values of the attributes.

Attributes

`end_state_trajectory`	The name of a .dcd trajectory file containing configurations generated by the simulation of the end state of the system.
`force_field_id`	The id of the force field parameters used to generate the data.
`free_energy_difference`	The free energy difference between the end state and the start state.
`property_phase`	The phase of the system (e.g.
`source_calculation_id`	The server id of the calculation which yielded this data.
`start_state_trajectory`	The name of a .dcd trajectory file containing configurations generated by the simulation of the start state of the system.
`substance`	A description of the composition of the stored system.
`thermodynamic_state`	The state at which the data was collected.
`topology_file_name`	The name of a coordinate file which encodes the topology of the system.

free_energy_difference

The free energy difference between the end state and the start state. The default value of this attribute is not set and must be set by the user..

Type: Observable

topology_file_name

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

Type: FilePath

start_state_trajectory

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

Type: FilePath

end_state_trajectory

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

Type: FilePath

classmethod most_information(stored_data_1: StoredFreeEnergyData, stored_data_2: StoredFreeEnergyData) → Optional[StoredFreeEnergyData][source]

A comparison function which will always retain both pieces of free energy data. At this time no situation can be envisaged that the same free energy data from exactly the same calculation will be store.

Parameters

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

to_storage_query()[source]

Returns: The storage query which would match this data object.
Return type: FreeEnergyDataQuery

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 –