stk.Multiply
- class stk.Multiply(coefficient, filter=<function Multiply.<lambda>>)[source]
Bases:
FitnessNormalizer
[T
]Multiplies the fitness values by some coefficient.
Examples
Multiplying Fitness Values by a Set of Coefficients
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 multiply each property by some coefficient, which reflects its relative importance to the final fitness value. For example if you multiply the value of one property by1
and another by2
, the second will contribute twice as much to the final fitness value, assuming that you get the final fitness value by using theSum
normalizer afterMultiply
.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: (1, 1, 1), } normalizer = stk.Multiply((1, 2, 3)) normalized_fitness_values = normalizer.normalize(fitness_values) assert np.all(np.equal( normalized_fitness_values[record], (1, 2, 3), ))
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: (1, 1, 1), record2: None, } normalizer = stk.Multiply( coefficient=(1, 2, 3), # 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], (1, 2, 3), )) assert normalized_fitness_values[record2] is None
- Parameters:
coefficient (float | list[float]) – The coefficients each fitness value is multiplied by. 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
orFalse
. Only molecules which returnTrue
will have fitness values normalized. By default, all molecules will have fitness values normalized. The instance passed to the fitness_values argument ofnormalize()
is passed as the first argument, while the second argument will be passed everyMoleculeRecord
in it, one at a time.
Methods
Normalize some fitness values.