Measurement

class cinnabar.measurements.Measurement(labelA: Hashable, labelB: Hashable, DG: Quantity | str, uncertainty: Quantity | str, computational: bool, source: str = '', temperature: Quantity | str = <Quantity(298.15, 'kelvin')>)

The free energy difference of moving from A to B

All quantities are accompanied by units, to prevent mix-ups associated with kcal and kJ. This is done via the openff.units package:

>>> m = Measurement(labelA='LigandA', labelB='LigandB',
...                 DG=2.4 * unit.kilocalorie_per_mol,
...                 uncertainty=0.2 * unit.kilocalorie_per_mol,
...                 computational=True,
...                 source='gromacs')

Alternatively strings are automatically coerced into quantities, making this equivalent to above:

>>> m = Measurement(labelA='LigandA', labelB='LigandB',
...                 DG='2.4 kcal/mol',
...                 uncertainty='0.2 kcal/mol',
...                 computational=True,
...                 source='gromacs')

Where a measurement is “absolute” then a ReferenceState can be used as the label at one end of the measurement. I.e. it is relative to a reference ground state. E.g. an absolute measurement for “LigandA” is defined as:

>>> m = Measurement(labelA=ReferenceState(), labelB='LigandA',
...                 DG=-11.2 * unit.kilocalorie_per_mol,
...                 uncertainty=0.3 * unit.kilocalorie_per_mol,
...                 computational=False)

Methods

from_experiment

Shortcut to create a Measurement from experimental data

Attributes

source	An arbitrary label to group measurements from a common source
temperature	298 K (298.15 * unit.kelvin)
labelA	Label of state A, e.g. a ligand name or any hashable Python object.
labelB	Label of state B
DG	The free energy difference of moving from A to B in kcal/mol
uncertainty	The uncertainty of the DG measurement in kcal/mol
computational	If this measurement is computationally based (or experimental)

DG: Quantity

The free energy difference of moving from A to B in kcal/mol

computational: bool

If this measurement is computationally based (or experimental)

classmethod from_experiment(label: str | Hashable, Ki: Quantity | str, uncertainty: Quantity | str = <Quantity(0, 'nanomolar')>, *, source: str = '', temperature: Quantity | str = <Quantity(298.15, 'kelvin')>)

Shortcut to create a Measurement from experimental data

Can perform conversion from Ki values to kcal/mol values.

Parameters:

• label (str | Hashable) – label for this data point.

• Ki (unit.Quantity | str) – experimental Ki value ex.: 500 * unit.nanomolar OR 0.5 * unit.micromolar or “0.5 * unit.nanomolar”

• uncertainty (unit.Quantity | str) – uncertainty of the experimental value default is zero if no uncertainty is provided (0 * unit.nanomolar)

• source (str, optional) – source of experimental measurement

• temperature (unit.Quantity | str, optional) – temperature in K at which the experimental measurement was carried out. By default: 298 K (298.15 * unit.kelvin)

labelA: Hashable

Label of state A, e.g. a ligand name or any hashable Python object

labelB: Hashable

Label of state B

source: str = ''

An arbitrary label to group measurements from a common source

temperature: Quantity = <Quantity(298.15, 'kelvin')>

298 K (298.15 * unit.kelvin)

Type:

Temperature that the measurement was taken at in K. By default

uncertainty: Quantity

The uncertainty of the DG measurement in kcal/mol