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.
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.
- returns
The storage query which would match this
validate
([attribute_type])Validate the values of the attributes.
Attributes
The name of a coordinate file which encodes the topology information of the system.
The id of the force field parameters used to generate the data.
The total number of molecules in the system.
A frame of observables collected over the duration of the simulation.
The phase of the system (e.g.
The server id of the calculation which yielded this data.
The statistical inefficiency of the collected data.
A description of the composition of the stored system.
The state at which the data was collected.
The name of a .dcd trajectory file containing configurations generated by the simulation.
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
classmethod
has_ancillary_data
()[source]¶ 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
-
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
-
to_storage_query
()[source]¶ - Returns
The storage query which would match this data object.
- Return type
-
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
-
json
(file_path=None, format=False)¶ Creates a JSON representation of this class.
-
classmethod
parse_json
(string_contents, encoding='utf8')¶ Parses a typed json string into the corresponding class structure.
-
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 –
-