Density

class openff.evaluator.properties.Density(thermodynamic_state=None, phase=PropertyPhase.Undefined, substance=None, value=None, uncertainty=None, source=None)[source]

A class representation of a density property

__init__(thermodynamic_state=None, phase=PropertyPhase.Undefined, substance=None, value=None, uncertainty=None, source=None)

Constructs a new PhysicalProperty object.

Parameters

thermodynamic_state (ThermodynamicState) – The thermodynamic state that the property was measured in.
phase (PropertyPhase) – The phase that the property was measured in.
substance (Substance) – The composition of the substance that was measured.
value (openff.evaluator.unit.Quantity) – The value of the measured physical property.
uncertainty (openff.evaluator.unit.Quantity) – The uncertainty in the measured value.
source (Source) – The source of this property.

Methods

`__init__`([thermodynamic_state, phase, ...])	Constructs a new PhysicalProperty object.
`default_reweighting_schema`([...])	Returns the default calculation schema to use when estimating this property by reweighting existing data.
`default_simulation_schema`([...])	Returns the default calculation schema to use when estimating this class of property from direct simulations.
`default_unit`()	openff.evaluator.unit.Unit: The default unit (e.g.
`from_json`(file_path)	Create this object from a JSON file.
`get_attributes`([attribute_type])	Returns all attributes of a specific attribute_type.
`json`([file_path, format])	Creates a JSON representation of this class.
`parse_json`(string_contents)	Parses a typed json string into the corresponding class structure.
`validate`([attribute_type])	Validate the values of the attributes.

Attributes

`gradients`	The gradients of this property with respect to different force field parameters.
`id`	A unique identifier string assigned to this property
`metadata`	Additional metadata associated with this property.
`phase`	The phase / phases that this property was measured in.
`source`	The original source of this physical property.
`substance`	The substance that this property was measured estimated for.
`thermodynamic_state`	The thermodynamic state that this propertywas measured / estimated at.
`uncertainty`	The uncertainty in measured / estimated value of this property.
`value`	The measured / estimated value of this property.

classmethod default_unit()[source]: openff.evaluator.unit.Unit: The default unit (e.g. g / mol) associated with this class of property.

static default_simulation_schema(absolute_tolerance=UNDEFINED, relative_tolerance=UNDEFINED, n_molecules=1000) → SimulationSchema[source]

Returns the default calculation schema to use when estimating this class of property from direct simulations.

Parameters

absolute_tolerance (openff.evaluator.unit.Quantity, optional) – The absolute tolerance to estimate the property to within.
relative_tolerance (float) – The tolerance (as a fraction of the properties reported uncertainty) to estimate the property to within.
n_molecules (int) – The number of molecules to use in the simulation.

Returns

The schema to follow when estimating this property.

Return type

SimulationSchema

static default_reweighting_schema(absolute_tolerance=UNDEFINED, relative_tolerance=UNDEFINED, n_effective_samples=50) → ReweightingSchema[source]

Returns the default calculation schema to use when estimating this property by reweighting existing data.

Parameters

absolute_tolerance (openff.evaluator.unit.Quantity, optional) – The absolute tolerance to estimate the property to within.
relative_tolerance (float) – The tolerance (as a fraction of the properties reported uncertainty) to estimate the property to within.
n_effective_samples (int) – The minimum number of effective samples to require when reweighting the cached simulation data.

Returns

The schema to follow when estimating this property.

Return type

ReweightingSchema

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

gradients

The gradients of this property with respect to different force field parameters. The default value of this attribute is not set. This attribute is optional.

Type: list

id

A unique identifier string assigned to this property

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

metadata

Additional metadata associated with this property. All property metadata will be made accessible to estimation workflows. The default value of this attribute is not set. This attribute is optional.

Type: dict

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

phase

The phase / phases that this property was measured in. The default value of this attribute is not set and must be set by the user..

Type: PropertyPhase

source

The original source of this physical property. The default value of this attribute is not set. This attribute is optional.

Type: Source

substance

The substance that this property was measured estimated for. The default value of this attribute is not set and must be set by the user..

Type: Substance

thermodynamic_state

The thermodynamic state that this propertywas measured / estimated at. The default value of this attribute is not set and must be set by the user..

Type: ThermodynamicState

uncertainty

The uncertainty in measured / estimated value of this property. The default value of this attribute is not set. This attribute is optional.

Type: Quantity

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 –

value

The measured / estimated value of this property. The default value of this attribute is not set and must be set by the user..

Type: Quantity