Measurement — cinnabar documentation

class cinnabar.measurements.Measurement(*, labelA: ~typing.Hashable, labelB: ~typing.Hashable, DG: ~openff.models.types.FloatQuantity, uncertainty: ~openff.models.types.FloatQuantity, temperature: ~openff.models.types.FloatQuantity = <Quantity(298.15, 'kelvin')>, computational: bool, source: str = '')[source]#

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

`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
`uncertainty`	The uncertainty of the DG measurement
`temperature`	Temperature that the measurement was taken as
`computational`	If this measurement is computationally based (or experimental)
`source`	An arbitrary label to group measurements from a common source

class Config[source]#

DG: FloatQuantity#: The free energy difference of moving from A to B

computational: bool#: If this measurement is computationally based (or experimental)

classmethod from_experiment(label: str | ~typing.Hashable, Ki: ~pint.Quantity, uncertainty: ~pint.Quantity = <Quantity(0, 'nanomolar')>, *, source: str = '', temperature: ~pint.Quantity = <Quantity(298.15, 'kelvin')>)[source]#

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) – experimental Ki value ex.: 500 * unit.nanomolar OR 0.5 * unit.micromolar
uncertainty (unit.Quantity) – 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, 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: FloatQuantity#: Temperature that the measurement was taken as

uncertainty: FloatQuantity#: The uncertainty of the DG measurement

Measurement#

`Measurement`#