def _get_case_data_1() -> CaseData:
topology_graph = stk.polymer.Linear(
building_blocks=(stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]), ),
repeating_unit='A',
num_repeating_units=2,
)
return CaseData(
fitness_normalizer=stk.ReplaceFitness(
get_replacement=lambda population: min(record.get_fitness_value()
for record in population
if record.get_fitness_value(
) is not None) / 2,
filter=lambda population, record: record.get_fitness_value() is
None,
),
population=(
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(1),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(2),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(3),
stk.MoleculeRecord(topology_graph),
),
normalized=(
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(1),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(2),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(3),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(0.5),
),
)
# Minimize synthetic accessibility and asymmetry.
# Maximise pore volume and window size.
fitness_normalizer = stk.TryCatch(
stk.Sequence(
save_fitness,
stk.Power([1, 1, -1, -1], filter=valid_fitness),
stk.DivideByMean(filter=valid_fitness),
stk.Multiply([5, 1, 10, 10], filter=valid_fitness),
stk.Sum(filter=valid_fitness),
# Replace all fitness values that are lists or None with
# a small value.
stk.ReplaceFitness(replacement_fn=lambda population: 1e-8,
filter=lambda p, m: isinstance(
p.get_fitness_values()[m],
(list, type(None)),
)),
),
stk.ReplaceFitness(replacement_fn=lambda population: 1e-8, ))
# #####################################################################
# Exit condition.
# #####################################################################
terminator = stk.NumGenerations(50)
# #####################################################################
# Make plotters.
# #####################################################################
def valid_fitness(population, mol):
return None not in population.get_fitness_values()[mol]
fitness_normalizer = stk.Sequence(
stk.Power([1, -1], filter=valid_fitness),
stk.DivideByMean(filter=valid_fitness),
stk.Multiply([1.0, 1.0], filter=valid_fitness),
stk.Sum(filter=valid_fitness),
stk.ReplaceFitness(
replacement_fn=lambda population:
min(
f for _, f in population.get_fitness_values().items()
if not isinstance(f, list)
) / 2,
filter=lambda p, m:
isinstance(p.get_fitness_values()[m], list),
)
)
# #####################################################################
# Exit condition.
# #####################################################################
terminator = stk.NumGenerations(60)
# #####################################################################
# Make plotters.
num_repeating_units=2,
)
topology_graph = stk.polymer.Linear(
building_blocks=(stk.BuildingBlock('BrCCBr', [stk.BromoFactory()]), ),
repeating_unit='A',
num_repeating_units=2,
)
@pytest.fixture(
params=(CaseData(
fitness_normalizer=stk.ReplaceFitness(
get_replacement=lambda population: min(record.get_fitness_value()
for record in population
if record.get_fitness_value(
) is not None) / 2,
filter=lambda population, record: record.get_fitness_value() is
None,
),
population=(
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(1),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(2),
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(3),
stk.MoleculeRecord(topology_graph),
),
normalized=(
stk.MoleculeRecord(
topology_graph=topology_graph, ).with_fitness_value(1),
