A candidate is the combination of a denoptim graph with molecular representation and may include also fitness/error, and possibly other stuff. More...

Inheritance diagram for denoptim.graph.Candidate:

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Public Member Functions
	Candidate ()

	Candidate (DGraph graph)

	Candidate (String name, DGraph graph)

	Candidate (String name, DGraph graph, double fitness, String uid, String smiles)

	Candidate (IAtomContainer iac, boolean useFragSpace) throws DENOPTIMException
	Builds a candidate from the SDF representation of an atom container. More...

	Candidate (IAtomContainer iac, boolean useFragSpace, boolean allowNoUID) throws DENOPTIMException
	Builds a candidate from the SDF representation of an atom container. More...

void	setChemicalRepresentation (IAtomContainer iac)
	Just place the argument in the IAtomContainer field of this object. More...

IAtomContainer	getChemicalRepresentation ()
	Returns the atom container representing this candidate. More...

IAtomContainer	getFitnessProviderOutputRepresentation () throws DENOPTIMException
	Returns an atom container representing this item in a way that is compatible for writing this item to an SDF file. More...

void	setComments (String str)

String	getComments ()

void	setSDFFile (String molFile)

void	setImageFile (String imgFile)

void	setGraph (DGraph graph)

void	setUID (String uid)

void	setSmiles (String smiles)

void	setFitness (double fitness)

void	setError (String error)

void	setName (String name)

String	getName ()

String	getError ()

String	getUID ()

String	getSmiles ()

String	getSDFFile ()

String	getImageFile ()

DGraph	getGraph ()

double	getFitness ()

boolean	hasFitness ()

void	setGeneration (int genId)

int	getGeneration ()
	The generation this candidate belong to is that in which it was generated. More...

void	setLevel (int lev)
	Sets level that generated this graph in a fragment space exploration experiment. More...

int	getLevel ()
	Returns the level that generated this graph in a fragment space exploration experiment. More...

int	compareTo (Candidate other)

String	toString ()

void	cleanup ()
	Clear the graph describing this candidate. More...

Candidate	clone ()

Static Public Member Functions
static Candidate	fromAtomContainerNoGraph (IAtomContainer iac, boolean allowNoUID) throws DENOPTIMException
	Wraps an atom container as a candidate even if a graph is not available. More...

Private Member Functions
	Candidate (String name, DGraph graph, String uid, String smiles, String molFile, String imgFile, String comment, int generationId, int level)

Private Attributes
String	uid
	Unique identifier of this candidate. More...

DGraph	graph
	Graph representation. More...

IAtomContainer	iac
	Chemical object representation. More...

String	smiles
	SMILES representation. More...

double	fitness
	fitness value More...

String	sdfFile
	Pathname to SDF file. More...

String	imgFile
	Pathname to an image (i.e., PNG file) More...

String	comment
	Any comments. More...

String	error
	Error that prevented calculation of the fitness. More...

boolean	hasFitness
	Flag signaling the presence of a fitness value associated. More...

int	generationId = -1
	ID of the generation at which this candidate was generated. More...

String	name
	Name of this candidate (not guaranteed to be unique) More...

int	level
	Level that generated this graph in fragment space exploration. More...

Detailed Description

A candidate is the combination of a denoptim graph with molecular representation and may include also fitness/error, and possibly other stuff.

Definition at line 39 of file Candidate.java.

Constructor & Destructor Documentation

◆ Candidate() [1/7]

denoptim.graph.Candidate.Candidate ( )

Definition at line 110 of file Candidate.java.

References denoptim.graph.Candidate.hasFitness, denoptim.graph.Candidate.name, denoptim.graph.Candidate.smiles, and denoptim.graph.Candidate.uid.

Referenced by denoptim.graph.Candidate.clone(), and denoptim.graph.Candidate.fromAtomContainerNoGraph().

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◆ Candidate() [2/7]

denoptim.graph.Candidate.Candidate ( DGraph graph )

Definition at line 120 of file Candidate.java.

References denoptim.graph.Candidate.graph, denoptim.graph.Candidate.hasFitness, denoptim.graph.DGraph.setCandidateOwner(), denoptim.graph.Candidate.smiles, and denoptim.graph.Candidate.uid.

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◆ Candidate() [3/7]

denoptim.graph.Candidate.Candidate	(	String	name,
		DGraph	graph
	)

Definition at line 132 of file Candidate.java.

References denoptim.graph.Candidate.graph, denoptim.graph.Candidate.hasFitness, denoptim.graph.Candidate.name, denoptim.graph.DGraph.setCandidateOwner(), denoptim.graph.Candidate.smiles, and denoptim.graph.Candidate.uid.

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◆ Candidate() [4/7]

denoptim.graph.Candidate.Candidate	(	String	name,
		DGraph	graph,
		double	fitness,
		String	uid,
		String	smiles
	)

Definition at line 145 of file Candidate.java.

References denoptim.graph.Candidate.fitness, denoptim.graph.Candidate.graph, denoptim.graph.Candidate.hasFitness, denoptim.graph.Candidate.name, denoptim.graph.DGraph.setCandidateOwner(), denoptim.graph.Candidate.smiles, and denoptim.graph.Candidate.uid.

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◆ Candidate() [5/7]

denoptim.graph.Candidate.Candidate	(	String	name,
		DGraph	graph,
		String	uid,
		String	smiles,
		String	molFile,
		String	imgFile,
		String	comment,
		int	generationId,
		int	level
	)

private

Definition at line 160 of file Candidate.java.

References denoptim.graph.Candidate.comment, denoptim.graph.Candidate.generationId, denoptim.graph.Candidate.graph, denoptim.graph.Candidate.imgFile, denoptim.graph.Candidate.level, denoptim.graph.Candidate.name, denoptim.graph.DGraph.setCandidateOwner(), denoptim.graph.Candidate.smiles, and denoptim.graph.Candidate.uid.

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◆ Candidate() [6/7]

denoptim.graph.Candidate.Candidate	(	IAtomContainer	iac,
		boolean	useFragSpace
	)		throws DENOPTIMException

Builds a candidate from the SDF representation of an atom container.

This method does interpret the properties of the atom container object and used them to define the various field values that define this candidate.

Parameters

iac	the container to read and interpret.
useFragSpace	set `true` to enable usage of the building block space when reading in the string-encoder graph representation of this object. Use `false` when a building block space is undefined and the graph representation can only be built assuming that there are as many APs as used in this graph, while other information on the graph building blocks cannot be inferred.

Exceptions

DENOPTIMException

Definition at line 193 of file Candidate.java.

References denoptim.graph.Candidate.iac.

◆ Candidate() [7/7]

denoptim.graph.Candidate.Candidate	(	IAtomContainer	iac,
		boolean	useFragSpace,
		boolean	allowNoUID
	)		throws DENOPTIMException

Builds a candidate from the SDF representation of an atom container.

This method does interpret the properties of the atom container object and used them to define the various field values that define this candidate.

Parameters

iac	the container to read and interpret.
useFragSpace	set `true` to enable usage of the building block space when reading in the string-encoder graph representation of this object. Use `false` when a building block space is undefined and the graph representation can only be built assuming that there are as many APs as used in this graph, while other information on the graph building blocks cannot be inferred.
allowNoUID	use `true` to allow creation on a candidate that has no unique identifier.

Exceptions

DENOPTIMException

Definition at line 217 of file Candidate.java.

References denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.constants.DENOPTIMConstants.GRAPHLEVELTAG, denoptim.graph.Candidate.iac, denoptim.utils.MoleculeUtils.makeSameAs(), denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.constants.DENOPTIMConstants.PROVENANCE, denoptim.io.DenoptimIO.readGraphFromSDFileIAC(), denoptim.graph.DGraph.setCandidateOwner(), denoptim.constants.DENOPTIMConstants.SMILESTAG, and denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG.

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Member Function Documentation

◆ cleanup()

void denoptim.graph.Candidate.cleanup ( )

Clear the graph describing this candidate.

Definition at line 670 of file Candidate.java.

References denoptim.graph.DGraph.cleanup(), and denoptim.graph.Candidate.graph.

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◆ clone()

Candidate denoptim.graph.Candidate.clone ( )

Definition at line 678 of file Candidate.java.

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◆ compareTo()

int denoptim.graph.Candidate.compareTo ( Candidate other )

Returns: a negative integer, 0, or a positive integer depending on whether this object is less than, equal to, or greater than the other object given as argument.

Definition at line 621 of file Candidate.java.

References denoptim.graph.Candidate.fitness, denoptim.graph.Candidate.graph, denoptim.graph.DGraph.graphId, and denoptim.graph.Candidate.hasFitness.

◆ fromAtomContainerNoGraph()

static Candidate denoptim.graph.Candidate.fromAtomContainerNoGraph	(	IAtomContainer	iac,
		boolean	allowNoUID
	)		throws DENOPTIMException

static

Wraps an atom container as a candidate even if a graph is not available.

Essentially, this method produces a candidate that has as much info as available in the atom container, but ignores the lack of a valid graph definition.

Parameters

iac	the atom container to be wrapped.
allowNoUID	use `true` to allow creation on a candidate that has no unique identifier.

Returns: a new candidate with no graph but with a molecular representation.

Exceptions

DENOPTIMException if the UID is required but not found.

Definition at line 301 of file Candidate.java.

References denoptim.graph.Candidate.Candidate(), denoptim.constants.DENOPTIMConstants.FITNESSTAG, denoptim.constants.DENOPTIMConstants.GRAPHLEVELTAG, denoptim.graph.Candidate.iac, denoptim.utils.MoleculeUtils.makeSameAs(), denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.constants.DENOPTIMConstants.PROVENANCE, denoptim.constants.DENOPTIMConstants.SMILESTAG, and denoptim.constants.DENOPTIMConstants.UNIQUEIDTAG.

Referenced by denoptim.gui.MoleculeViewPanel.loadChemicalStructureFromFile().

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◆ getChemicalRepresentation()

IAtomContainer denoptim.graph.Candidate.getChemicalRepresentation ( )

Returns the atom container representing this candidate.

Returns: the atom container.

Definition at line 389 of file Candidate.java.

References denoptim.graph.Candidate.iac.

Referenced by denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), and denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ getComments()

String denoptim.graph.Candidate.getComments ( )

Definition at line 438 of file Candidate.java.

References denoptim.graph.Candidate.comment.

Referenced by denoptim.gui.MoleculeViewPanel.fillDataTable().

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◆ getError()

String denoptim.graph.Candidate.getError ( )

Definition at line 509 of file Candidate.java.

References denoptim.graph.Candidate.error.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), and denoptim.gui.MoleculeViewPanel.fillDataTable().

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◆ getFitness()

double denoptim.graph.Candidate.getFitness ( )

Definition at line 551 of file Candidate.java.

References denoptim.graph.Candidate.fitness.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.ga.Population.getMaxFitness(), denoptim.ga.Population.getMinFitness(), denoptim.ga.Population.getMinFitnessMember(), denoptim.ga.EAUtils.outputPopulationDetails(), denoptim.ga.SelectionHelper.performRWS(), and denoptim.ga.SelectionHelper.performTournamentSelection().

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◆ getFitnessProviderOutputRepresentation()

IAtomContainer denoptim.graph.Candidate.getFitnessProviderOutputRepresentation ( ) throws DENOPTIMException

Returns an atom container representing this item in a way that is compatible for writing this item to an SDF file.

Returns: a decorated atom container.

Exceptions

DENOPTIMException when conversion of graph to json fails.

Definition at line 402 of file Candidate.java.

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◆ getGeneration()

int denoptim.graph.Candidate.getGeneration ( )

The generation this candidate belong to is that in which it was generated.

In asynchronous experiments, the generation at which a candidate is generated and that when it enters the population may be different.

Returns: the generation at which a candidate is generated.

Definition at line 578 of file Candidate.java.

References denoptim.graph.Candidate.generationId.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), and denoptim.gui.MoleculeViewPanel.fillDataTable().

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◆ getGraph()

DGraph denoptim.graph.Candidate.getGraph ( )

Definition at line 544 of file Candidate.java.

References denoptim.graph.Candidate.graph.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.fitnessevaluator.FitnessEvaluationTask.call(), denoptim.task.FitnessTask.FitnessTask(), denoptim.ga.Population.getXoverPartners(), denoptim.ga.EvolutionaryAlgorithm.makeOffspringB(), denoptim.ga.EAUtils.outputPopulationDetails(), denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_Free(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FreeBackwards(), denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ getImageFile()

String denoptim.graph.Candidate.getImageFile ( )

Definition at line 537 of file Candidate.java.

References denoptim.graph.Candidate.imgFile.

Referenced by denoptim.ga.EAUtils.outputFinalResults().

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◆ getLevel()

int denoptim.graph.Candidate.getLevel ( )

Returns the level that generated this graph in a fragment space exploration experiment.

Returns: the level that generated this graph in a fragment space exploration experiment.

Definition at line 603 of file Candidate.java.

References denoptim.graph.Candidate.level.

◆ getName()

String denoptim.graph.Candidate.getName ( )

Definition at line 502 of file Candidate.java.

References denoptim.graph.Candidate.name.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.OffspringEvaluationTask.call(), denoptim.ga.PopulationTest.compareSizeOfSites(), denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.ga.Population.getXoverPartners(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.ga.EAUtils.outputFinalResults(), denoptim.ga.EAUtils.outputPopulationDetails(), denoptim.ga.EAUtils.readCandidateFromFile(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runInternalFitness(), and denoptim.programs.moldecularmodelbuilder.MolecularModelBuilder.runProgram().

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◆ getSDFFile()

String denoptim.graph.Candidate.getSDFFile ( )

Definition at line 530 of file Candidate.java.

References denoptim.graph.Candidate.sdfFile.

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.outputFinalResults(), denoptim.ga.EAUtils.outputPopulationDetails(), and denoptim.gui.MoleculeViewPanel.showPopup().

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◆ getSmiles()

String denoptim.graph.Candidate.getSmiles ( )

Definition at line 523 of file Candidate.java.

References denoptim.graph.Candidate.smiles.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), and denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask().

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◆ getUID()

String denoptim.graph.Candidate.getUID ( )

Definition at line 516 of file Candidate.java.

References denoptim.graph.Candidate.uid.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), and denoptim.ga.EAUtils.outputPopulationDetails().

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◆ hasFitness()

boolean denoptim.graph.Candidate.hasFitness ( )

Definition at line 558 of file Candidate.java.

References denoptim.graph.Candidate.hasFitness.

◆ setChemicalRepresentation()

void denoptim.graph.Candidate.setChemicalRepresentation ( IAtomContainer iac )

Just place the argument in the IAtomContainer field of this object.

We do not read and interpret the input argument as done in Candidate(IAtomContainer) or Candidate(IAtomContainer, boolean).

Parameters

iac	new value of IAtomContainer field

Definition at line 378 of file Candidate.java.

References denoptim.graph.Candidate.iac.

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.graph.Candidate.clone(), denoptim.ga.EAUtils.readCandidateFromFile(), denoptim.task.FitnessTask.runExternalFitness(), and denoptim.task.FitnessTask.runFitnessProvider().

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◆ setComments()

void denoptim.graph.Candidate.setComments ( String str )

Definition at line 431 of file Candidate.java.

◆ setError()

void denoptim.graph.Candidate.setError ( String error )

Definition at line 488 of file Candidate.java.

References denoptim.graph.Candidate.error.

Referenced by denoptim.graph.Candidate.clone(), denoptim.task.FitnessTask.runExternalFitness(), and denoptim.task.FitnessTask.runInternalFitness().

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◆ setFitness()

void denoptim.graph.Candidate.setFitness ( double fitness )

Definition at line 480 of file Candidate.java.

References denoptim.graph.Candidate.fitness.

Referenced by denoptim.graph.Candidate.clone(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.task.FitnessTask.runInternalFitness(), denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph(), denoptim.ga.PopulationTest.testGetMinMax(), denoptim.ga.PopulationTest.testIsInPercentile(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ setGeneration()

void denoptim.graph.Candidate.setGeneration ( int genId )

Definition at line 565 of file Candidate.java.

References denoptim.graph.Candidate.generationId.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), and denoptim.io.DenoptimIO.readCandidates().

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◆ setGraph()

void denoptim.graph.Candidate.setGraph ( DGraph graph )

Definition at line 459 of file Candidate.java.

References denoptim.graph.Candidate.graph.

Referenced by denoptim.combinatorial.GraphBuildingTask.call().

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◆ setImageFile()

void denoptim.graph.Candidate.setImageFile ( String imgFile )

Definition at line 452 of file Candidate.java.

References denoptim.graph.Candidate.imgFile.

Referenced by denoptim.task.FitnessTask.runFitnessProvider().

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◆ setLevel()

void denoptim.graph.Candidate.setLevel ( int lev )

Sets level that generated this graph in a fragment space exploration experiment.

Parameters

lev	the level index

Definition at line 590 of file Candidate.java.

References denoptim.graph.Candidate.level.

◆ setName()

void denoptim.graph.Candidate.setName ( String name )

Definition at line 495 of file Candidate.java.

References denoptim.graph.Candidate.name.

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.ga.EAUtils.readCandidateFromFile(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

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◆ setSDFFile()

void denoptim.graph.Candidate.setSDFFile ( String molFile )

Definition at line 445 of file Candidate.java.

Referenced by denoptim.ga.EAUtils.outputFinalResults(), denoptim.io.DenoptimIO.readCandidates(), denoptim.task.FitnessTask.runFitnessProvider(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ setSmiles()

void denoptim.graph.Candidate.setSmiles ( String smiles )

Definition at line 473 of file Candidate.java.

References denoptim.graph.Candidate.smiles.

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.ga.EAUtils.readCandidateFromFile(), and denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider().

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◆ setUID()

void denoptim.graph.Candidate.setUID ( String uid )

Definition at line 466 of file Candidate.java.

References denoptim.graph.Candidate.uid.

Referenced by denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.OffspringEvaluationTask.OffspringEvaluationTask(), denoptim.ga.EAUtils.readCandidateFromFile(), denoptim.task.FitnessTask.runExternalFitness(), denoptim.combinatorial.GraphBuildingTask.sendToFitnessProvider(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ toString()

String denoptim.graph.Candidate.toString ( )

Definition at line 650 of file Candidate.java.

References denoptim.graph.Candidate.fitness, denoptim.graph.Candidate.name, denoptim.graph.Candidate.sdfFile, and denoptim.graph.Candidate.uid.

Member Data Documentation

◆ comment

String denoptim.graph.Candidate.comment

private

Any comments.

Definition at line 79 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), and denoptim.graph.Candidate.getComments().

◆ error

String denoptim.graph.Candidate.error

private

Error that prevented calculation of the fitness.

Definition at line 84 of file Candidate.java.

Referenced by denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getError(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), and denoptim.graph.Candidate.setError().

◆ fitness

double denoptim.graph.Candidate.fitness

private

fitness value

Definition at line 64 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.compareTo(), denoptim.graph.Candidate.getFitness(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.graph.Candidate.setFitness(), and denoptim.graph.Candidate.toString().

◆ generationId

int denoptim.graph.Candidate.generationId = -1

private

ID of the generation at which this candidate was generated.

This may not be the generation at which this candidate entered the population!

Definition at line 95 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getGeneration(), and denoptim.graph.Candidate.setGeneration().

◆ graph

DGraph denoptim.graph.Candidate.graph

private

Graph representation.

Definition at line 49 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.cleanup(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.compareTo(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.graph.Candidate.getGraph(), and denoptim.graph.Candidate.setGraph().

◆ hasFitness

boolean denoptim.graph.Candidate.hasFitness

private

Flag signaling the presence of a fitness value associated.

Definition at line 89 of file Candidate.java.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.compareTo(), denoptim.gui.MoleculeViewPanel.fillDataTable(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), and denoptim.graph.Candidate.hasFitness().

◆ iac

IAtomContainer denoptim.graph.Candidate.iac

private

Chemical object representation.

Definition at line 54 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.fromAtomContainerNoGraph(), denoptim.graph.Candidate.getChemicalRepresentation(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), and denoptim.graph.Candidate.setChemicalRepresentation().

◆ imgFile

String denoptim.graph.Candidate.imgFile

private

Pathname to an image (i.e., PNG file)

Definition at line 74 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getImageFile(), and denoptim.graph.Candidate.setImageFile().

◆ level

int denoptim.graph.Candidate.level

private

Level that generated this graph in fragment space exploration.

Definition at line 105 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getLevel(), and denoptim.graph.Candidate.setLevel().

◆ name

String denoptim.graph.Candidate.name

private

Name of this candidate (not guaranteed to be unique)

Definition at line 100 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.graph.Candidate.getName(), denoptim.graph.Candidate.setName(), and denoptim.graph.Candidate.toString().

◆ sdfFile

String denoptim.graph.Candidate.sdfFile

private

Pathname to SDF file.

Definition at line 69 of file Candidate.java.

Referenced by denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getSDFFile(), and denoptim.graph.Candidate.toString().

◆ smiles

String denoptim.graph.Candidate.smiles

private

SMILES representation.

Definition at line 59 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.graph.Candidate.getSmiles(), and denoptim.graph.Candidate.setSmiles().

◆ uid

String denoptim.graph.Candidate.uid

private

Unique identifier of this candidate.

Definition at line 44 of file Candidate.java.

Referenced by denoptim.graph.Candidate.Candidate(), denoptim.graph.Candidate.clone(), denoptim.graph.Candidate.getFitnessProviderOutputRepresentation(), denoptim.graph.Candidate.getUID(), denoptim.graph.Candidate.setUID(), and denoptim.graph.Candidate.toString().

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

/github/workspace/src/main/java/denoptim/graph/Candidate.java

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Candidate() [1/7]

◆ Candidate() [2/7]

◆ Candidate() [3/7]

◆ Candidate() [4/7]

◆ Candidate() [5/7]

◆ Candidate() [6/7]

◆ Candidate() [7/7]

Member Function Documentation

◆ cleanup()

◆ clone()

◆ compareTo()

◆ fromAtomContainerNoGraph()

◆ getChemicalRepresentation()

◆ getComments()

◆ getError()

◆ getFitness()

◆ getFitnessProviderOutputRepresentation()

◆ getGeneration()

◆ getGraph()

◆ getImageFile()

◆ getLevel()

◆ getName()

◆ getSDFFile()

◆ getSmiles()

◆ getUID()

◆ hasFitness()

◆ setChemicalRepresentation()

◆ setComments()

◆ setError()

◆ setFitness()

◆ setGeneration()

◆ setGraph()

◆ setImageFile()

◆ setLevel()

◆ setName()

◆ setSDFFile()

◆ setSmiles()

◆ setUID()

◆ toString()

Member Data Documentation

◆ comment

◆ error

◆ fitness

◆ generationId

◆ graph

◆ hasFitness

◆ iac

◆ imgFile

◆ level

◆ name

◆ sdfFile

◆ smiles

◆ uid