Replace Fitness

class ReplaceFitness(get_replacement, filter=<function ReplaceFitness.<lambda>>)[source]

Bases: stk.ea.fitness_normalizers.fitness_normalizer.FitnessNormalizer

Replaces fitness values of a certain value with a new value.

Examples

Giving a Fitness Value to Failed Calculations

You want to replace fitness values which are None with half the minimum fitness value in the population. A fitness value may be None because the fitness calculation failed for some reason.

import stk

building_block = stk.BuildingBlock(
    smiles='BrCCBr',
    functional_groups=[stk.BromoFactory()],
)

population = (
    stk.MoleculeRecord(
        topology_graph=stk.polymer.Linear(
            building_blocks=(building_block, ),
            repeating_unit='A',
            num_repeating_units=2,
        ),
    ).with_fitness_value(
        fitness_value=2,
        normalized=False,
    ),
    # This will have a fitness value of None.
    stk.MoleculeRecord(
        topology_graph=stk.polymer.Linear(
            building_blocks=(building_block, ),
            repeating_unit='A',
            num_repeating_units=2,
        ),
    ),
)

def get_minimum_fitness_value(population):
    return min(
        record.get_fitness_value() for record in population
        if record.get_fitness_value() is not None
    )

replacer = stk.ReplaceFitness(
    # The replacement is half the minimum fitness value in the
    # population.
    get_replacement=lambda population:
        get_minimum_fitness_value(population) / 2,
    # Only replace fitness values which are None.
    filter=lambda population, record:
        record.get_fitness_value() is None,
)

# Use the replacer.
normalized_population = tuple(replacer.normalize(population))
normalized_record1, normalized_record2 = normalized_population
assert normalized_record1.get_fitness_value() == 2
assert normalized_record2.get_fitness_value() == 1

Methods

normalize(population)

Normalize the fitness values in population.

__init__(get_replacement, filter=<function ReplaceFitness.<lambda>>)[source]

Initialize a ReplaceFitness instance.

Parameters
  • get_replacement (callable) – Takes a single parameter, a tuple of MoleculeRecord instances, which needs to be normalized. The entire population passed to normalize() is passed to this parameter, regardless of what is passed to the filter parameter. The callable returns the value which is to be given to the normalized records.

  • filter (callable, optional) – Takes two parameters, first is a tuple of MoleculeRecord instances, and the second is a MoleculeRecord. The callable 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 population argument of normalize() is passed as the first argument, while the second argument will be passed every MoleculeRecord in it, one at a time.

normalize(population)[source]

Normalize the fitness values in population.

Parameters

population (tuple of MoleculeRecord) – The molecules which need to have their fitness values normalized.

Yields

MoleculeRecord – A record with a normalized fitness value.