DENOPTIM's (internal) fitness provider calculates the value of Variables that are used in an expression for calculating a single numerical results, i.e., the fitness. More...

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Public Member Functions
	FitnessProvider (List< DescriptorForFitness > descriptors, String expression, Logger logger)
	Constructs an instance that will calculate the fitness according to the given parameters. More...

double	getFitness (IAtomContainer iac) throws Exception
	Calculated the fitness according to the current configuration. More...

Protected Attributes
DescriptorEngine	engine
	The engine that collects and calculates descriptors. More...

Private Member Functions
double	processValue (String descName, DescriptorForFitness descriptor, IDescriptor implementation, IImplementationSpecification descSpec, DescriptorValue value, String varName, IAtomContainer iac) throws Exception
	Takes the value and checks that it is all good, then processes the value to extract the result defined by the DescriptorForFitness, puts a human-readable version in the molecular representation, and the numerical value for fitness calculation in the appropriate map. More...

Private Attributes
List< DescriptorForFitness >	descriptors
	The collection of descriptors to consider. More...

String	expression
	The equation used to calculate the fitness value. More...

Logger	logger = null
	Program-specific logger. More...

Detailed Description

DENOPTIM's (internal) fitness provider calculates the value of Variables that are used in an expression for calculating a single numerical results, i.e., the fitness.

Each the value of each Variable derived from the calculation of DescriptorForFitness for a specific chemical object.

Author: Marco Foscato

Definition at line 70 of file FitnessProvider.java.

Constructor & Destructor Documentation

◆ FitnessProvider()

denoptim.fitness.FitnessProvider.FitnessProvider	(	List< DescriptorForFitness >	descriptors,
		String	expression,
		Logger	logger
	)

Constructs an instance that will calculate the fitness according to the given parameters.

Note that the descriptors implementation instances are not the same (not same hash) than those that will be used to compute the descriptor values. This to make the descriptor calculations thread-safe. Any parameter that is set to the descriptors argument is copied into the new instances of the descriptor implementations.

Parameters

descriptors	the list of descriptors to calculate in order to calculate the fitness value
expression	the string defining in expression-language format the mathematical formulation used to calculate the fitness from the descriptor values.

Definition at line 109 of file FitnessProvider.java.

References denoptim.fitness.DescriptorForFitness.cloneAllButImpl(), denoptim.fitness.FitnessProvider.descriptors, denoptim.fitness.FitnessProvider.engine, denoptim.fitness.FitnessProvider.expression, denoptim.fitness.DescriptorForFitness.getClassName(), and denoptim.fitness.FitnessProvider.logger.

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Member Function Documentation

◆ getFitness()

double denoptim.fitness.FitnessProvider.getFitness ( IAtomContainer iac ) throws Exception

Calculated the fitness according to the current configuration.

The values of the descriptors, as well as the fitness value, are added to the properties of the atom container.

Parameters

iac	the chemical object to evaluate.

Returns: the final value of the fitness.

Exceptions

Exception if an error occurs during calculation of the descriptor or any initial configuration was missing/wrong.

Definition at line 164 of file FitnessProvider.java.

References denoptim.fitness.FitnessProvider.descriptors, denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.fitness.FitnessProvider.engine, denoptim.fitness.FitnessProvider.expression, denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.utils.ManySMARTSQuery.getAllMatches(), denoptim.utils.ManySMARTSQuery.getMessage(), denoptim.utils.ManySMARTSQuery.getProblem(), denoptim.fitness.DescriptorForFitness.getVariables(), denoptim.utils.ManySMARTSQuery.hasProblems(), denoptim.fitness.FitnessProvider.logger, denoptim.utils.MathUtils.mean(), denoptim.fitness.FitnessProvider.processValue(), denoptim.utils.DummyAtomHandler.removeDummy(), denoptim.utils.DummyAtomHandler.removeDummyInHapto(), and denoptim.fitness.DescriptorForFitness.shortName.

Referenced by denoptim.task.FitnessTask.runInternalFitness(), denoptim.fitness.FitnessProviderTest.testGetConstantFitness(), denoptim.fitness.FitnessProviderTest.testGetFitness(), denoptim.fitness.FitnessProviderTest.testGetFitnessWithCustomDescriptors(), and denoptim.fitness.FitnessProviderTest.testGetFitnessWithParametrizedDescriptors().

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◆ processValue()

double denoptim.fitness.FitnessProvider.processValue	(	String	descName,
		DescriptorForFitness	descriptor,
		IDescriptor	implementation,
		IImplementationSpecification	descSpec,
		DescriptorValue	value,
		String	varName,
		IAtomContainer	iac
	)		throws Exception

private

Takes the value and checks that it is all good, then processes the value to extract the result defined by the DescriptorForFitness, puts a human-readable version in the molecular representation, and the numerical value for fitness calculation in the appropriate map.

Exceptions

Exception

Definition at line 491 of file FitnessProvider.java.

Referenced by denoptim.fitness.FitnessProvider.getFitness().

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Member Data Documentation

◆ descriptors

List<DescriptorForFitness> denoptim.fitness.FitnessProvider.descriptors

private

The collection of descriptors to consider.

Definition at line 80 of file FitnessProvider.java.

Referenced by denoptim.fitness.FitnessProvider.FitnessProvider(), and denoptim.fitness.FitnessProvider.getFitness().

◆ engine

DescriptorEngine denoptim.fitness.FitnessProvider.engine

protected

The engine that collects and calculates descriptors.

Definition at line 75 of file FitnessProvider.java.

Referenced by denoptim.fitness.FitnessProvider.FitnessProvider(), denoptim.fitness.FitnessProvider.getFitness(), and denoptim.fitness.FitnessProviderTest.testConfigureDescriptorsList().

◆ expression

String denoptim.fitness.FitnessProvider.expression

private

The equation used to calculate the fitness value.

Definition at line 85 of file FitnessProvider.java.

Referenced by denoptim.fitness.FitnessProvider.FitnessProvider(), and denoptim.fitness.FitnessProvider.getFitness().

◆ logger

Logger denoptim.fitness.FitnessProvider.logger = null

private

Program-specific logger.

Definition at line 90 of file FitnessProvider.java.

Referenced by denoptim.fitness.FitnessProvider.FitnessProvider(), and denoptim.fitness.FitnessProvider.getFitness().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/fitness/FitnessProvider.java

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FitnessProvider()

Member Function Documentation

◆ getFitness()

◆ processValue()

Member Data Documentation

◆ descriptors

◆ engine

◆ expression

◆ logger