stk.Sum

class stk.Sum(filter=<function Sum.<lambda>>)

Bases: FitnessNormalizer[T]

Combines fitness value components into a single fitness value.

Examples

Combining Fitness Value Components Into a Single Value

Sometimes, your FitnessCalculator will return a fitness value which is a tuple of multiple numbers. Each number represents a different property of the molecule, which contributes to the final fitness value. This fitness normalizer combines these fitness value components into a single number, by taking their sum.

import stk

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: (1, -2, 3),
}
sum_normalizer = stk.Sum()
normalized_fitness_values = sum_normalizer.normalize(
    fitness_values=fitness_values,
)
assert normalized_fitness_values[record] == 2

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

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, -2, 3),
    record2: None,
}
normalizer = stk.Sum(
    # 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 normalized_fitness_values[record1] == 2
assert normalized_fitness_values[record2] is None

Parameters:

filter (Callable[[dict[T, Any], T], bool]) – A function wihch 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]