stk.Power

class stk.Power(power, filter=<function Power.<lambda>>)

Bases: FitnessNormalizer[T]

Raises fitness values to some power.

Examples

Raising Fitness Values to a Power

Sometimes you might calculate a property for a molecule, where that property indicates a low fitness value. You can use Power to raise it to the power of -1 to get your final fitness value

import stk

building_block = stk.BuildingBlock('BrCCBr', stk.BromoFactory())
record1 = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
record2 = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
fitness_values = {
    record1: 1,
    record2: 2,
}
normalizer = stk.Power(-1)
normalized_fitness_values = normalizer.normalize(fitness_values)
assert normalized_fitness_values[record1] == 1
assert normalized_fitness_values[record2] == 0.5

Raising Fitness Values by a Set of Powers

In this example, assume that each fitness value consists of a tuple of numbers, each representing a different property of the molecule, and each contributing to the final fitness value. The properties can be anything, such as energy, number of atoms or diameter.

If your final fitness value depends on the combination of these properties, you will probably first want to scale them with DivideByMean. Once this is done, you may want to raise each property by some power. For example if you raise the value of one property by 1 and another by -1, it means that when the value of property 1 is big, the fitness value should also be big, but if the value of property 2 is big, the fitness value should be small.

Giving a concrete example

import stk
import numpy as np

building_block = stk.BuildingBlock('BrCCBr', stk.BromoFactory())
record = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
fitness_values = {
    record: (2, 2, 2),
}
normalizer = stk.Power((1, -1, 2))
normalized_fitness_values = normalizer.normalize(fitness_values)
assert np.all(np.equal(
    normalized_fitness_values[record],
    (2, 0.5, 4),
))

Selectively Normalizing Fitness Values

Sometimes, you only want to normalize some members of a population, for example if some do not have an assigned fitness value, because the fitness calculation failed for whatever reason. You can use the filter parameter to exclude records from the normalization

import stk
import numpy as np

building_block = stk.BuildingBlock('BrCCBr', stk.BromoFactory())
record1 = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
record2 = stk.MoleculeRecord(
    topology_graph=stk.polymer.Linear(
        building_blocks=[building_block],
        repeating_unit='A',
        num_repeating_units=2,
    ),
)
fitness_values = {
    record1: (2, 2, 2),
    record2: None,
}
normalizer = stk.Power(
    power=(1, -1, 2),
    # Only normalize values which are not None.
    filter=lambda fitness_values, record:
        fitness_values[record] is not None,
)
normalized_fitness_values = normalizer.normalize(fitness_values)
assert np.all(np.equal(
    normalized_fitness_values[record1],
    (2, 0.5, 4),
))
assert normalized_fitness_values[record2] is None

Parameters:

• power (float | list[float]) – The power each fitness value is raised to. Can be a single number or multiple numbers, depending on the form of the fitness value.

• filter (Callable[[dict[T, Any], T], bool]) – A function which returns True or False. Only molecules which return True will have fitness values normalized. By default, all molecules will have fitness values normalized. The instance passed to the fitness_values argument of normalize() is passed as the first argument, while the second argument will be passed every MoleculeRecord in it, one at a time.

Methods

normalize

Normalize some fitness values.

normalize(fitness_values)

Normalize some fitness values.

Parameters:

fitness_values (dict[T, Any]) – The molecules which need to have their fitness values normalized.

Returns:

The new fitness value for each molecule.

Return type:

dict[T, Any]