Property Data Sets
PhysicalPropertyDataSet is a collection of measured physical properties encapsulated as
physical property objects. They may be created from scratch:
# Define a density measurement density = Density( substance=Substance.from_components("O"), thermodynamic_state=ThermodynamicState( pressure=1.0*unit.atmospheres, temperature=298.15*unit.kelvin ), phase=PropertyPhase.Liquid, value=1.0*unit.gram/unit.millilitre, uncertainty=0.0001*unit.gram/unit.millilitre ) # Add the property to a data set data_set = PhysicalPropertyDataset() data_set.add_properties(density)
are readily JSON (de)serializable:
# Save the data set as a JSON file. data_set.json(file_path="data_set.json", format=True) # Load the data set from a JSON file data_set = PhysicalPropertyDataset.from_json(file_path="data_set.json")
and may be converted to pandas
The framework implements specific data set objects for extracting data measurements directly from a number of open data
sources, such as the
ThermoMLDataSet (see ThermoML Archive) which provides utilities for extracting the data
from the NIST ThermoML Archive and converting it into the standard framework
Data set objects are directly iterable:
for physical_property in data_set: ...
or can be iterated over for a specific substance:
for physical_property in data_set.properties_by_substance(substance): ...
or for a specific type of property:
for physical_property in data_set.properties_by_type("Density"): ...
PhysicalProperty object is a base class for any object which describes a measured property of substance, and is
defined by a combination of:
the observed value of the property.
Substancespecifying the substance that the measurement was collected for.
PropertyPhasespecifying the phase that the measurement was collected in.
ThermodynamicStatespecifying the thermodynamic conditions under which the measurement was performed
as well as optionally
the uncertainty in the value of the property.
a list of
ParameterGradientwhich defines the gradient of the property with respect to the model parameters if it was computationally estimated.
Sourcespecifying the source (either experimental or computational) and provenance of the measurement.
Each type of property supported by the framework, such as a density of an enthalpy of vaporization, must have it’s own
class representation which inherits from
# Define a density measurement density = Density( substance=Substance.from_components("O"), thermodynamic_state=ThermodynamicState( pressure=1.0*unit.atmospheres, temperature=298.15*unit.kelvin ), phase=PropertyPhase.Liquid, value=1.0*unit.gram/unit.millilitre, uncertainty=0.0001*unit.gram/unit.millilitre )
Substance is defined by a number of components (which may have specific roles assigned to them such as
being solutes in the system) and the amount of each component in the substance.
To create a pure substance containing only water:
water_substance = Substance.from_components("O")
To create binary mixture of water and methanol in a 20:80 ratio:
binary_mixture = Substance() binary_mixture.add_component(Component(smiles="O"), MoleFraction(value=0.2)) binary_mixture.add_component(Component(smiles="CO"), MoleFraction(value=0.8))
To create a substance of an infinitely dilute paracetamol solute dissolved in water:
solution = Substance() solution.add_component( Component(smiles="O", role=Component.Role.Solvent), MoleFraction(value=1.0) ) solution.add_component( Component(smiles="CC(=O)Nc1ccc(O)cc1", role=Component.Role.Solute), ExactAmount(value=1) )
PropertyPhase enum describes the possible phases which a measurement was performed in.
While the enum only has three defined phases (
Gas), multiple phases can be formed by
OR’ing (|) multiple phases together. As an example, to define a phase for a liquid and gas coexisting:
liquid_gas_phase = PropertyPhase.Liquid | PropertyPhase.Gas
ThermodynamicState specifies a combination of the temperature and (optionally) the pressure at which a
measurement is performed:
thermodynamic_state = ThermodynamicState( temperature=298.15*unit.kelvin, pressure=1.0*unit.atmosphere )