Parameters for genetic algorithm. More...

Inheritance diagram for denoptim.programs.denovo.GAParameters:

Collaboration diagram for denoptim.programs.denovo.GAParameters:

Public Member Functions
	GAParameters ()
	Constructor. More...

String	getUIDFileIn ()

String	getUIDFileOut ()

String	getVisitedGraphsFile ()

String	getInterfaceDir ()

String	getMonitorFile ()

int	getMonitorDumpStep ()

int	getPrecisionLevel ()

int	getNumberOfCPU ()

boolean	isSortOrderDecreasing ()

int	getMaxTriesFactor ()

int	getMaxGeneticOpAttempts ()

String	getDataDirectory ()

void	setWorkingDirectory (String pathName)

int	getReplacementStrategy ()

boolean	parentsSurvive ()

double	getCrowdingFactorSteepSigma ()

double	getCrowdingFactorMiddleSigma ()

double	getCrowdingMultiplier ()

int	getCrowdingProbabilityScheme ()

double	getGrowthFactorSteepSigma ()

double	getGrowthFactorMiddleSigma ()

double	getGrowthMultiplier ()

int	getGrowthProbabilityScheme ()

double	getMolGrowthFactorSteepSigma ()

double	getMolGrowthFactorMiddleSigma ()

double	getMolGrowthMultiplier ()

int	getMolGrowthProbabilityScheme ()

void	setPopulationSize (int size)

int	getPopulationSize ()

int	getNumberOfGenerations ()

String	getSelectionStrategy ()

List< MutationType >	getExcludedMutationTypes ()

int	getSelectionStrategyType ()

int	getNumberOfConvergenceGenerations ()

int	getNumberOfChildren ()

double	getCrossoverWeight ()

int	maxOffsprintFromXover ()

boolean	keepBestSibling ()

double	getMutationWeight ()

double	getConstructionWeight ()

double	getSymmetryProbability ()

String	getInitialPopulationFile ()

String	getInitMolsToFragmentFile ()

double[]	getMultiSiteMutationWeights ()

boolean	useMolSizeBasedProb ()

boolean	useLevelBasedProb ()

int	getParallelizationScheme ()

double	getMinFitnessSD ()

boolean	dumpMonitor ()

double	getSaveRingSystemsFitnessThreshold ()

boolean	getSaveRingSystemsAsTemplatesNonScaff ()

boolean	getSaveRingSystemsAsTemplatesScaff ()

boolean	coupleMutationAndCrossover ()

void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

void	processParameters () throws DENOPTIMException
	Processes currently loaded fields. More...

void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

boolean	savePopFile ()

int	getMaxRingsAddedByMutation ()
	Return the value of the number of rings that we are allowed to add in a single `MutationType#ADDRING` mutation. More...

Public Member Functions inherited from denoptim.programs.RunTimeParameters
	RunTimeParameters (ParametersType paramType)
	Constructor. More...

String	paramTypeName ()
	Returns a string defining the type the parameters collected here. More...

String	getWorkDirectory ()
	Gets the pathname to the working directory. More...

void	setWorkDirectory (String pathname)
	Gets the pathname to the working directory. More...

String	getLogFilePathname ()
	Gets the pathname to the log file. More...

void	setLogFilePathname (String pathname)
	Sets the pathname to the log file. More...

Logger	getLogger ()
	Get the name of the program specific logger. More...

Logger	startProgramSpecificLogger (String loggerIdentifier) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startProgramSpecificLogger (String loggerIdentifier, boolean toLogFile) throws SecurityException, IOException
	Starts a logger with the given name. More...

Logger	startConsoleLogger (String loggerIdentifier)
	Starts a program-specific logger that prints to System.err stream. More...

int	getVerbosity ()
	Returns the level of verbosity, i.e., the amount of log that we want to print. More...

void	setVerbosity (int l)
	Set the level of verbosity. More...

Randomizer	getRandomizer ()
	Returns the current program-specific randomizer. More...

long	getRandomSeed ()
	Returns the seed. More...

void	setRandomizer (Randomizer rng)
	Sets the randomizer. More...

Randomizer	startRandomizer ()
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

Randomizer	startRandomizer (long seed)
	Starts a program specific randomizer, i.e., a tool for generating random numbers and taking random decisions. More...

void	readParameterFile (String infile) throws DENOPTIMException
	Read the parameter TXT file line by line and interpret its content. More...

void	readParameterLine (String line) throws DENOPTIMException

boolean	containsParameters (ParametersType type)

RunTimeParameters	getParameters (ParametersType type)

void	setParameters (RunTimeParameters otherParams)

void	interpretKeyword (String line) throws DENOPTIMException
	Processes a string looking for keyword and a possibly associated value. More...

abstract void	interpretKeyword (String key, String value) throws DENOPTIMException
	Processes a keyword/value pair and assign the related parameters. More...

abstract void	checkParameters () throws DENOPTIMException
	Evaluate consistency of input parameters. More...

abstract void	processParameters () throws DENOPTIMException
	Processes all parameters and initialize related objects. More...

abstract String	getPrintedList ()
	Returns the list of parameters in a string with newline characters as delimiters. More...

void	printParameters ()
	Print all parameters. More...

Static Public Member Functions
static int	convertProbabilityScheme (String option) throws DENOPTIMException

Static Public Member Functions inherited from denoptim.programs.RunTimeParameters
static boolean	readYesNoTrueFalse (String s)
	Reads a string searching for any common way to say either yes/true (including shorthand t/y) or no/false (including shorthand f/n either). More...

Public Attributes
String	timeStamp = "NOTIMESTAMP"
	Time stamp identifying this run. More...

int	maxUIDMemory = 1000000
	Maximum number of unique identifiers kept in memory. More...

String	uidMemoryOnDisk = "memory_UIDs.txt"
	Text file used to store unique identifiers beyond the limits of the memory (see `GAParameters#maxUIDMemory`). More...

boolean	mutatedGraphFailedEvalTolerant = true
	Flag that enables the ignoring of mutated graphs that lead to a failure in the evaluation of graphs that generates SMILES, InChI and molecular representation. More...

boolean	xoverGraphFailedEvalTolerant = true
	Flag that enables the ignoring of crossover-ed graphs that lead to a f ailure in the evaluation of graphs that generates SMILES, InChI and molecular representation. More...

boolean	xoverFailureTolerant = true
	Flag that enables the ignoring of crossover events triggering exceptions. More...

boolean	mutationFailureTolerant = true
	Flag that enables the ignoring of mutation events triggering exceptions. More...

boolean	buildAnewFailureTolerant = true
	Flag that enables the ignoring of construction from scratch events triggering exceptions. More...

int	maxXOverableSubGraphSize = 20
	Limit to the size of subgraphs that are exchanged during crossover. More...

Public Attributes inherited from denoptim.programs.RunTimeParameters
final String	NL = System.getProperty("line.separator")
	New line character. More...

Protected Attributes
String	initPoplnFile = ""
	Pathname of the initial population file. More...

String	initMolsToFragmentFile = null
	Pathname to the file collecting molecules to fragment to generate initial population. More...

String	uidFileIn = ""
	Pathname of the file with the list of individuals unique identifiers that are initially known. More...

String	uidFileOut = ""
	Pathname of the file where the individuals unique identifiers will be recorded. More...

String	visitedGraphsFile = "GRAPHS.txt"
	Pathname to the file containing the list of previously visited graph. More...

int	populationSize = 50
	Size of the population. More...

int	numOfChildren = 5
	Number of children (i.e., new offspring) to be produced in each generation. More...

int	numConvGen = 5
	Number of identical generations before convergence is reached. More...

int	numGenerations = 100
	Maximum number of generations to run for. More...

int	maxTriesPerPop = 25
	Factor controlling the maximum number of attempts to build a graph so that the maximum number of attempts = factor * population size. More...

int	maxGeneticOpAttempts = 100
	Maximum number of attempts to perform any genetic operation (i.e., either crossover or mutation) on any parents before giving up. More...

int	replacementStrategy = 1
	Replacement strategy: 1) replace worst individuals with new ones that are better than the worst, 2) no replacement (the population keeps growing). More...

boolean	parentsSurvive = true
	Flag defining if population members can survive multiple generations (when this variable is `true`) or the population is refreshed at every generation (when this variable is `false`). More...

int	lvlGrowthProbabilityScheme = 0
	Definition of the growth probability function: More...

double	lvlGrowthMultiplier = 0.5
	Parameter controlling the growth probability function of types 'EXP_DIFF' and 'TANH'. More...

double	lvlGrowthSigmaSteepness = 1.0
	Parameters controlling the growth probability function of type 'SIGMA': steepness of the function where p=50%. More...

double	lvlGrowthSigmaMiddle = 2.5
	Parameters controlling the growth probability function of type 'SIGMA': level at which p=50% (can be a float) More...

boolean	useLevelBasedProb = false
	Flag recording the intention to use level-controlled graph extension probability. More...

boolean	useMolSizeBasedProb = false
	Flag recording the intention to use molecular size-controlled graph extension probability. More...

int	molGrowthProbabilityScheme = 2
	Definition of the molGrowth probability function: More...

double	molGrowthMultiplier = 0.5
	Parameter controlling the molGrowth probability function of types 'EXP_DIFF' and 'TANH'. More...

double	molGrowthSigmaSteepness = 0.2
	Parameters controlling the molGrowth probability function of type 'SIGMA': steepness of the function where p=50%. More...

double	molGrowthSigmaMiddle = 25
	Parameters controlling the molGrowth probability function of type 'SIGMA': level at which p=50% (can be a float) More...

int	crowdingProbabilityScheme = 3
	Definition of the crowding probability function. More...

double	crowdingMultiplier = 0.5
	Parameter controlling the crowding probability function of types 'EXP_DIFF' and 'TANH'. More...

double	crowdingSigmaSteepness = 1.0
	Parameters controlling the crowding probability function of type 'SIGMA': steepness of the function where p=50%. More...

double	crowdingSigmaMiddle = 2.5
	Parameters controlling the crowding probability function of type 'SIGMA': level at which p=50% (can be a float) More...

double	symmetricSubProbability = 0.8
	The probability at which symmetric substitution occurs. More...

double	mutationWeight = 1.0
	The relative weight at which mutation is performed. More...

boolean	coupleMutationAndCrossover = false
	Flag defining if we want mutation to occur on offspring that result from crossover (i.e., mutation and crossover are coupled), otherwise we want to mutate population members irrespectively on crossover. More...

double	builtAnewWeight = 1.0
	The relative weight at which construction from scratch is performed. More...

double	crossoverWeight = 1.0
	The relative weight at which crossover is performed. More...

int	xoverSelectionMode = 3
	Crossover parents selection strategy: integer code. More...

String	strXoverSelectionMode = xoverSelectionMode+""
	Crossover parents selection strategy: string. More...

int	maxOffsprintFromXover = 1
	Number of offspring that a single crossover operation can produce. More...

boolean	keepBestSibling = false
	Flag controlling if we choose the best sibling out of crossover. More...

long	seed = 0L
	The seed value for random number generation. More...

int	parallelizationScheme = 1
	Parallelization scheme: synchronous or asynchronous. More...

int	numParallelTasks = 0
	Maximum number of parallel tasks. More...

boolean	sortOrderDecreasing = true
	Flag controlling how to sort the population based on the fitness. More...

int	precisionLevel = 3
	Precision for reporting the value of the fitness. More...

int	monitorDumpStep = 50
	Monitor dumps step. More...

boolean	dumpMonitor = false
	Flag controlling if we dump monitored data or not. More...

double	minFitnessSD = 0.000001
	Minimal standard deviation accepted in the fitness values of the initial population. More...

int	maxRingsAddedByMutation = 1
	Maximum number of rings added by a single mutation operation. More...

boolean	saveRingSystemsAsTemplatesScaffolds = false
	Flag controlling the possibility of collecting cyclic graph systems that include a scaffold and save them as new template scaffolds. More...

boolean	saveRingSystemsAsTemplatesNonScaff = false
	Flag controlling the possibility of collecting cyclic graph systems that do NOT include a scaffold and save them as new template non-scaffold building blocks. More...

double	saveRingSystemsFitnessThreshold = 0.10
	Fitness threshold for adding template to building block libraries. More...

boolean	writePopOnDisk = false
	Flag requesting to write a SDF file that collects all the population members each time we report the population details on file. More...

Protected Attributes inherited from denoptim.programs.RunTimeParameters
boolean	isMaster = true
	Flag signaling this is the master collection of parameters. More...

String	workDir = System.getProperty("user.dir")
	Working directory. More...

String	logFile = "unset"
	Log file. More...

int	verbosity = 0
	Verbosity level for logger. More...

Map< ParametersType, RunTimeParameters >	otherParameters
	Collection of other parameters by type. More...

Package Attributes
List< MutationType >	excludedMutationTypes = new ArrayList<MutationType>()
	Mutation types that are excluded everywhere. More...

Private Member Functions
void	createWorkingDirectory () throws DENOPTIMException
	Create the directory that will store the output of the GA run. More...

Private Attributes
String	dataDir = System.getProperty("user.dir")
	Pathname to the working directory for the current run. More...

String	interfaceDir
	Pathname to the interface directory for the current run. More...

String	monitorFile = ""
	Pathname of file where EA monitors dumps are printed. More...

final String	DEFUIDFILEOUTNAME = "MOLUID.txt"
	Default name of the UIDFileOut. More...

double[]	mutliSiteMutationWeights = new double[]{0,10,1}
	The weights of multi-site mutations. More...

Additional Inherited Members
Protected Member Functions inherited from denoptim.programs.RunTimeParameters
void	checkOtherParameters () throws DENOPTIMException
	Checks any of the parameter collections contained in this instance. More...

void	processOtherParameters () throws DENOPTIMException
	Processes any of the parameter collections contained in this instance. More...

void	ensureFileExistsIfSet (String pathname)
	Ensures a pathname is not empty nor null and that it does lead to an existing file or triggers an error. More...

void	ensureFileExists (String pathname)
	Ensures a pathname does lead to an existing file or triggers an error. More...

void	ensureNotNull (String paramName, String param, String paramKey)
	Ensures that a parameter is not null or triggers an error. More...

void	ensureIsPositive (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureIsPositiveOrZero (String paramName, int value, String paramKey)
	Ensures that a parameter is a positive number (x>=0) or triggers an error. More...

void	ensureInRange (String paramName, int value, int min, int max, String paramKey)
	Ensures that a parameter is within a range or triggers an error. More...

Detailed Description

Parameters for genetic algorithm.

Author: Vishwesh Venkatraman; Marco Foscato

Definition at line 45 of file GAParameters.java.

Constructor & Destructor Documentation

◆ GAParameters()

denoptim.programs.denovo.GAParameters.GAParameters ( )

Constructor.

Parameters

paramType

Definition at line 422 of file GAParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.GA_PARAMS.

Member Function Documentation

◆ checkParameters()

void denoptim.programs.denovo.GAParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 1445 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GARunner.runProgram().

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◆ convertProbabilityScheme()

static int denoptim.programs.denovo.GAParameters.convertProbabilityScheme ( String option ) throws DENOPTIMException

static

Definition at line 1343 of file GAParameters.java.

Referenced by denoptim.gui.GAParametersForm.createCrowdProbDataset(), denoptim.gui.GAParametersForm.createLvlProbDataset(), denoptim.gui.GAParametersForm.createMolSizeProbDataset(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

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◆ coupleMutationAndCrossover()

boolean denoptim.programs.denovo.GAParameters.coupleMutationAndCrossover ( )

Returns: true if we want mutation to occur on offspring that result from crossover, otherwise we want to mutate population members irrespectively on crossover.

Definition at line 824 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.coupleMutationAndCrossover.

◆ createWorkingDirectory()

void denoptim.programs.denovo.GAParameters.createWorkingDirectory ( ) throws DENOPTIMException

private

Create the directory that will store the output of the GA run.

Exceptions

DENOPTIMException

Definition at line 1375 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.dataDir, denoptim.files.FileFormat.GA_RUN, denoptim.programs.denovo.GAParameters.interfaceDir, denoptim.programs.denovo.GAParameters.setWorkingDirectory(), and denoptim.programs.denovo.GAParameters.timeStamp.

Referenced by denoptim.programs.denovo.GAParameters.processParameters().

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◆ dumpMonitor()

boolean denoptim.programs.denovo.GAParameters.dumpMonitor ( )

Definition at line 790 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.dumpMonitor.

◆ getConstructionWeight()

double denoptim.programs.denovo.GAParameters.getConstructionWeight ( )

Definition at line 723 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.builtAnewWeight.

Referenced by denoptim.ga.EAUtils.chooseGenerationMethod(), and denoptim.ga.EvolutionaryAlgorithm.makeOffspringB().

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◆ getCrossoverWeight()

double denoptim.programs.denovo.GAParameters.getCrossoverWeight ( )

Definition at line 687 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.crossoverWeight.

Referenced by denoptim.ga.EAUtils.chooseGenerationMethod(), and denoptim.ga.EvolutionaryAlgorithm.makeOffspringB().

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◆ getCrowdingFactorMiddleSigma()

double denoptim.programs.denovo.GAParameters.getCrowdingFactorMiddleSigma ( )

Definition at line 554 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.crowdingSigmaMiddle.

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

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◆ getCrowdingFactorSteepSigma()

double denoptim.programs.denovo.GAParameters.getCrowdingFactorSteepSigma ( )

Definition at line 547 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.crowdingSigmaSteepness.

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

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◆ getCrowdingMultiplier()

double denoptim.programs.denovo.GAParameters.getCrowdingMultiplier ( )

Definition at line 561 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.crowdingMultiplier.

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

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◆ getCrowdingProbabilityScheme()

int denoptim.programs.denovo.GAParameters.getCrowdingProbabilityScheme ( )

Definition at line 568 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.crowdingProbabilityScheme.

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

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◆ getDataDirectory()

String denoptim.programs.denovo.GAParameters.getDataDirectory ( )

Definition at line 506 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.dataDir.

Referenced by denoptim.ga.EAUtils.getPathNameToFinalPopulationDetailsFile(), denoptim.ga.EAUtils.getPathNameToFinalPopulationFolder(), denoptim.ga.EAUtils.getPathNameToGenerationDetailsFile(), denoptim.ga.EAUtils.getPathNameToGenerationFolder(), and denoptim.programs.denovo.GAParametersTest.testLogging().

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◆ getExcludedMutationTypes()

List< MutationType > denoptim.programs.denovo.GAParameters.getExcludedMutationTypes ( )

Definition at line 659 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.excludedMutationTypes.

◆ getGrowthFactorMiddleSigma()

double denoptim.programs.denovo.GAParameters.getGrowthFactorMiddleSigma ( )

Definition at line 582 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.lvlGrowthSigmaMiddle.

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

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◆ getGrowthFactorSteepSigma()

double denoptim.programs.denovo.GAParameters.getGrowthFactorSteepSigma ( )

Definition at line 575 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.lvlGrowthSigmaSteepness.

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

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◆ getGrowthMultiplier()

double denoptim.programs.denovo.GAParameters.getGrowthMultiplier ( )

Definition at line 589 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.lvlGrowthMultiplier.

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

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◆ getGrowthProbabilityScheme()

int denoptim.programs.denovo.GAParameters.getGrowthProbabilityScheme ( )

Definition at line 596 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.lvlGrowthProbabilityScheme.

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

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◆ getInitialPopulationFile()

String denoptim.programs.denovo.GAParameters.getInitialPopulationFile ( )

Definition at line 737 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.initPoplnFile.

◆ getInitMolsToFragmentFile()

String denoptim.programs.denovo.GAParameters.getInitMolsToFragmentFile ( )

Returns: the pathname to the file defining molecules to convert into candidates by fragmentation.

Definition at line 748 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.initMolsToFragmentFile.

Referenced by denoptim.ga.EvolutionaryAlgorithm.initializePopulation().

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◆ getInterfaceDir()

String denoptim.programs.denovo.GAParameters.getInterfaceDir ( )

Definition at line 450 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.interfaceDir.

Referenced by denoptim.programs.denovo.GARunner.runProgram().

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◆ getMaxGeneticOpAttempts()

int denoptim.programs.denovo.GAParameters.getMaxGeneticOpAttempts ( )

Definition at line 499 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.maxGeneticOpAttempts.

◆ getMaxRingsAddedByMutation()

int denoptim.programs.denovo.GAParameters.getMaxRingsAddedByMutation ( )

Return the value of the number of rings that we are allowed to add in a single MutationType#ADDRING mutation.

Returns: the maximum number of rings added in a single mutation.

Definition at line 1580 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.maxRingsAddedByMutation.

◆ getMaxTriesFactor()

int denoptim.programs.denovo.GAParameters.getMaxTriesFactor ( )

Definition at line 492 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.maxTriesPerPop.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), and denoptim.ga.EvolutionaryAlgorithm.processInitialPopCandidate().

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◆ getMinFitnessSD()

double denoptim.programs.denovo.GAParameters.getMinFitnessSD ( )

Definition at line 783 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.minFitnessSD.

Referenced by denoptim.ga.EvolutionaryAlgorithm.run().

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◆ getMolGrowthFactorMiddleSigma()

double denoptim.programs.denovo.GAParameters.getMolGrowthFactorMiddleSigma ( )

Definition at line 610 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.molGrowthSigmaMiddle.

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

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◆ getMolGrowthFactorSteepSigma()

double denoptim.programs.denovo.GAParameters.getMolGrowthFactorSteepSigma ( )

Definition at line 603 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.molGrowthSigmaSteepness.

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

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◆ getMolGrowthMultiplier()

double denoptim.programs.denovo.GAParameters.getMolGrowthMultiplier ( )

Definition at line 617 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.molGrowthMultiplier.

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

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◆ getMolGrowthProbabilityScheme()

int denoptim.programs.denovo.GAParameters.getMolGrowthProbabilityScheme ( )

Definition at line 624 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.molGrowthProbabilityScheme.

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

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◆ getMonitorDumpStep()

int denoptim.programs.denovo.GAParameters.getMonitorDumpStep ( )

Definition at line 464 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.monitorDumpStep.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), and denoptim.ga.EvolutionaryAlgorithm.initializePopulation().

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◆ getMonitorFile()

String denoptim.programs.denovo.GAParameters.getMonitorFile ( )

Definition at line 457 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.monitorFile.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), and denoptim.ga.EvolutionaryAlgorithm.run().

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◆ getMultiSiteMutationWeights()

double[] denoptim.programs.denovo.GAParameters.getMultiSiteMutationWeights ( )

Definition at line 755 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.mutliSiteMutationWeights.

Referenced by denoptim.programs.denovo.GAParametersTest.testInterpretationOfKeywords().

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◆ getMutationWeight()

double denoptim.programs.denovo.GAParameters.getMutationWeight ( )

Definition at line 716 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.mutationWeight.

Referenced by denoptim.ga.EAUtils.chooseGenerationMethod(), and denoptim.ga.EvolutionaryAlgorithm.makeOffspringB().

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◆ getNumberOfChildren()

int denoptim.programs.denovo.GAParameters.getNumberOfChildren ( )

Definition at line 680 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.numOfChildren.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation().

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◆ getNumberOfConvergenceGenerations()

int denoptim.programs.denovo.GAParameters.getNumberOfConvergenceGenerations ( )

Definition at line 673 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.numConvGen.

Referenced by denoptim.ga.EvolutionaryAlgorithm.run().

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◆ getNumberOfCPU()

int denoptim.programs.denovo.GAParameters.getNumberOfCPU ( )

Definition at line 478 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.numParallelTasks.

Referenced by denoptim.ga.EvolutionaryAlgorithm.EvolutionaryAlgorithm(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EvolutionaryAlgorithm.processInitialPopCandidate(), and denoptim.ga.EvolutionaryAlgorithm.submitSyncParallelBatch().

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◆ getNumberOfGenerations()

int denoptim.programs.denovo.GAParameters.getNumberOfGenerations ( )

Definition at line 645 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.numGenerations.

Referenced by denoptim.ga.EAUtils.getPathNameToGenerationDetailsFile(), denoptim.ga.EAUtils.getPathNameToGenerationFolder(), and denoptim.ga.EvolutionaryAlgorithm.run().

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◆ getParallelizationScheme()

int denoptim.programs.denovo.GAParameters.getParallelizationScheme ( )

Definition at line 776 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.parallelizationScheme.

Referenced by denoptim.ga.EvolutionaryAlgorithm.EvolutionaryAlgorithm().

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◆ getPopulationSize()

int denoptim.programs.denovo.GAParameters.getPopulationSize ( )

Definition at line 638 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.populationSize.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), denoptim.ga.EvolutionaryAlgorithm.processInitialPopCandidate(), denoptim.ga.EvolutionaryAlgorithm.run(), and denoptim.ga.Population.trim().

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◆ getPrecisionLevel()

int denoptim.programs.denovo.GAParameters.getPrecisionLevel ( )

Definition at line 471 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.precisionLevel.

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

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◆ getPrintedList()

String denoptim.programs.denovo.GAParameters.getPrintedList ( )

Returns the list of parameters in a string with newline characters as delimiters.

Returns: the list of parameters in a string with newline characters as delimiters.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 1537 of file GAParameters.java.

References denoptim.programs.RunTimeParameters.NL, denoptim.programs.RunTimeParameters.otherParameters, and denoptim.programs.RunTimeParameters.paramTypeName().

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◆ getReplacementStrategy()

int denoptim.programs.denovo.GAParameters.getReplacementStrategy ( )

Definition at line 529 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.replacementStrategy.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), and denoptim.ga.EvolutionaryAlgorithm.run().

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◆ getSaveRingSystemsAsTemplatesNonScaff()

boolean denoptim.programs.denovo.GAParameters.getSaveRingSystemsAsTemplatesNonScaff ( )

Definition at line 804 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.saveRingSystemsAsTemplatesNonScaff.

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

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◆ getSaveRingSystemsAsTemplatesScaff()

boolean denoptim.programs.denovo.GAParameters.getSaveRingSystemsAsTemplatesScaff ( )

Definition at line 811 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.saveRingSystemsAsTemplatesScaffolds.

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

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◆ getSaveRingSystemsFitnessThreshold()

double denoptim.programs.denovo.GAParameters.getSaveRingSystemsFitnessThreshold ( )

Definition at line 797 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.saveRingSystemsFitnessThreshold.

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

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◆ getSelectionStrategy()

String denoptim.programs.denovo.GAParameters.getSelectionStrategy ( )

Definition at line 652 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.strXoverSelectionMode.

◆ getSelectionStrategyType()

int denoptim.programs.denovo.GAParameters.getSelectionStrategyType ( )

Definition at line 666 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.xoverSelectionMode.

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

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◆ getSymmetryProbability()

double denoptim.programs.denovo.GAParameters.getSymmetryProbability ( )

Definition at line 730 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.symmetricSubProbability.

◆ getUIDFileIn()

String denoptim.programs.denovo.GAParameters.getUIDFileIn ( )

Definition at line 429 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.uidFileIn.

◆ getUIDFileOut()

String denoptim.programs.denovo.GAParameters.getUIDFileOut ( )

Definition at line 436 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.uidFileOut.

Referenced by denoptim.ga.EvolutionaryAlgorithm.EvolutionaryAlgorithm(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), and denoptim.ga.EvolutionaryAlgorithm.processInitialPopCandidate().

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◆ getVisitedGraphsFile()

String denoptim.programs.denovo.GAParameters.getVisitedGraphsFile ( )

Definition at line 443 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.visitedGraphsFile.

◆ interpretKeyword()

void denoptim.programs.denovo.GAParameters.interpretKeyword	(	String	key,
		String	value
	)		throws DENOPTIMException

Processes a keyword/value pair and assign the related parameters.

Parameters

key	the keyword as string
value	the value as a string

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 838 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParametersTest.testInterpretationOfKeywords(), and denoptim.programs.denovo.GAParametersTest.testYesNoTrueFalseKeyword().

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◆ isSortOrderDecreasing()

boolean denoptim.programs.denovo.GAParameters.isSortOrderDecreasing ( )

Definition at line 485 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.sortOrderDecreasing.

◆ keepBestSibling()

boolean denoptim.programs.denovo.GAParameters.keepBestSibling ( )

Returns: true if we want to keep only the best among the two sibling that result from a single crossover.

Definition at line 709 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.keepBestSibling.

◆ maxOffsprintFromXover()

int denoptim.programs.denovo.GAParameters.maxOffsprintFromXover ( )

Returns: the maximum number of offspring produced by a single crossover operation.

Definition at line 698 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.maxOffsprintFromXover.

◆ parentsSurvive()

boolean denoptim.programs.denovo.GAParameters.parentsSurvive ( )

Returns: the flag controlling if parents are allowed to survive multiple generation or not.

Definition at line 540 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.parentsSurvive.

◆ processParameters()

void denoptim.programs.denovo.GAParameters.processParameters ( ) throws DENOPTIMException

Processes currently loaded fields.

Exceptions

DENOPTIMException typically due to I/O exception.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 1403 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GARunner.runProgram(), and denoptim.programs.denovo.GAParametersTest.testLogging().

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◆ savePopFile()

boolean denoptim.programs.denovo.GAParameters.savePopFile ( )

Returns: true if we are configures to save all population members each time we report the population details on file.

Definition at line 1568 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.writePopOnDisk.

◆ setPopulationSize()

void denoptim.programs.denovo.GAParameters.setPopulationSize ( int size )

Definition at line 631 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.populationSize.

Referenced by denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ setWorkingDirectory()

void denoptim.programs.denovo.GAParameters.setWorkingDirectory ( String pathName )

Definition at line 513 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.dataDir, denoptim.programs.denovo.GAParameters.DEFUIDFILEOUTNAME, denoptim.programs.denovo.GAParameters.interfaceDir, denoptim.programs.RunTimeParameters.logFile, denoptim.programs.denovo.GAParameters.monitorFile, and denoptim.programs.denovo.GAParameters.uidFileOut.

Referenced by denoptim.programs.denovo.GAParameters.createWorkingDirectory(), denoptim.programs.denovo.GARunner.runProgram(), denoptim.programs.denovo.GAParametersTest.testLogging(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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◆ useLevelBasedProb()

boolean denoptim.programs.denovo.GAParameters.useLevelBasedProb ( )

Definition at line 769 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.useLevelBasedProb.

◆ useMolSizeBasedProb()

boolean denoptim.programs.denovo.GAParameters.useMolSizeBasedProb ( )

Definition at line 762 of file GAParameters.java.

References denoptim.programs.denovo.GAParameters.useMolSizeBasedProb.

Member Data Documentation

◆ buildAnewFailureTolerant

boolean denoptim.programs.denovo.GAParameters.buildAnewFailureTolerant = true

Flag that enables the ignoring of construction from scratch events triggering exceptions.

Such events will still be recorded in the GA run Monitor.

Definition at line 403 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ builtAnewWeight

double denoptim.programs.denovo.GAParameters.builtAnewWeight = 1.0

protected

The relative weight at which construction from scratch is performed.

Definition at line 255 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getConstructionWeight(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ coupleMutationAndCrossover

boolean denoptim.programs.denovo.GAParameters.coupleMutationAndCrossover = false

protected

Flag defining if we want mutation to occur on offspring that result from crossover (i.e., mutation and crossover are coupled), otherwise we want to mutate population members irrespectively on crossover.

Definition at line 250 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.coupleMutationAndCrossover(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ crossoverWeight

double denoptim.programs.denovo.GAParameters.crossoverWeight = 1.0

protected

The relative weight at which crossover is performed.

Definition at line 260 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getCrossoverWeight(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ crowdingMultiplier

double denoptim.programs.denovo.GAParameters.crowdingMultiplier = 0.5

protected

Parameter controlling the crowding probability function of types 'EXP_DIFF' and 'TANH'.

Definition at line 220 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getCrowdingMultiplier(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ crowdingProbabilityScheme

int denoptim.programs.denovo.GAParameters.crowdingProbabilityScheme = 3

protected

Definition of the crowding probability function.

By default, the probability of using an AP that is hosted on an atom that already has an used AP is 100%.

Definition at line 214 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getCrowdingProbabilityScheme(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ crowdingSigmaMiddle

double denoptim.programs.denovo.GAParameters.crowdingSigmaMiddle = 2.5

protected

Parameters controlling the crowding probability function of type 'SIGMA': level at which p=50% (can be a float)

Definition at line 232 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getCrowdingFactorMiddleSigma(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ crowdingSigmaSteepness

double denoptim.programs.denovo.GAParameters.crowdingSigmaSteepness = 1.0

protected

Parameters controlling the crowding probability function of type 'SIGMA': steepness of the function where p=50%.

Definition at line 226 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getCrowdingFactorSteepSigma(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ dataDir

String denoptim.programs.denovo.GAParameters.dataDir = System.getProperty("user.dir")

private

Pathname to the working directory for the current run.

Definition at line 55 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.createWorkingDirectory(), denoptim.programs.denovo.GAParameters.getDataDirectory(), denoptim.programs.denovo.GAParameters.processParameters(), and denoptim.programs.denovo.GAParameters.setWorkingDirectory().

◆ DEFUIDFILEOUTNAME

final String denoptim.programs.denovo.GAParameters.DEFUIDFILEOUTNAME = "MOLUID.txt"

private

Default name of the UIDFileOut.

Definition at line 96 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.setWorkingDirectory().

◆ dumpMonitor

boolean denoptim.programs.denovo.GAParameters.dumpMonitor = false

protected

Flag controlling if we dump monitored data or not.

Definition at line 321 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.dumpMonitor(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ excludedMutationTypes

List<MutationType> denoptim.programs.denovo.GAParameters.excludedMutationTypes = new ArrayList<MutationType>()

package

Mutation types that are excluded everywhere.

Definition at line 285 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getExcludedMutationTypes(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.processParameters().

◆ initMolsToFragmentFile

String denoptim.programs.denovo.GAParameters.initMolsToFragmentFile = null

protected

Pathname to the file collecting molecules to fragment to generate initial population.

Definition at line 74 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getInitMolsToFragmentFile(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ initPoplnFile

String denoptim.programs.denovo.GAParameters.initPoplnFile = ""

protected

Pathname of the initial population file.

The file itself can be an SDF or a list of pathnames

Definition at line 68 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getInitialPopulationFile(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ interfaceDir

String denoptim.programs.denovo.GAParameters.interfaceDir

private

Initial value:

= dataDir

+ System.getProperty("file.separator") + "interface"

denoptim.programs.denovo.GAParameters.dataDir

String dataDir

Pathname to the working directory for the current run.

Definition: GAParameters.java:55

Pathname to the interface directory for the current run.

This is the pathname that is watched for external instructions

Definition at line 61 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.createWorkingDirectory(), denoptim.programs.denovo.GAParameters.getInterfaceDir(), and denoptim.programs.denovo.GAParameters.setWorkingDirectory().

◆ keepBestSibling

boolean denoptim.programs.denovo.GAParameters.keepBestSibling = false

protected

Flag controlling if we choose the best sibling out of crossover.

Definition at line 280 of file GAParameters.java.

Referenced by denoptim.ga.OffspringEvaluationTask.call(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.keepBestSibling().

◆ lvlGrowthMultiplier

double denoptim.programs.denovo.GAParameters.lvlGrowthMultiplier = 0.5

protected

Parameter controlling the growth probability function of types 'EXP_DIFF' and 'TANH'.

Definition at line 160 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getGrowthMultiplier(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ lvlGrowthProbabilityScheme

int denoptim.programs.denovo.GAParameters.lvlGrowthProbabilityScheme = 0

protected

Definition of the growth probability function:

Definition at line 154 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getGrowthProbabilityScheme(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ lvlGrowthSigmaMiddle

double denoptim.programs.denovo.GAParameters.lvlGrowthSigmaMiddle = 2.5

protected

Parameters controlling the growth probability function of type 'SIGMA': level at which p=50% (can be a float)

Definition at line 172 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getGrowthFactorMiddleSigma(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ lvlGrowthSigmaSteepness

double denoptim.programs.denovo.GAParameters.lvlGrowthSigmaSteepness = 1.0

protected

Parameters controlling the growth probability function of type 'SIGMA': steepness of the function where p=50%.

Definition at line 166 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getGrowthFactorSteepSigma(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ maxGeneticOpAttempts

int denoptim.programs.denovo.GAParameters.maxGeneticOpAttempts = 100

protected

Maximum number of attempts to perform any genetic operation (i.e., either crossover or mutation) on any parents before giving up.

Definition at line 134 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMaxGeneticOpAttempts(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ maxOffsprintFromXover

int denoptim.programs.denovo.GAParameters.maxOffsprintFromXover = 1

protected

Number of offspring that a single crossover operation can produce.

Definition at line 275 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.maxOffsprintFromXover().

◆ maxRingsAddedByMutation

int denoptim.programs.denovo.GAParameters.maxRingsAddedByMutation = 1

protected

Maximum number of rings added by a single mutation operation.

Definition at line 331 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMaxRingsAddedByMutation(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ maxTriesPerPop

int denoptim.programs.denovo.GAParameters.maxTriesPerPop = 25

protected

Factor controlling the maximum number of attempts to build a graph so that the maximum number of attempts = factor * population size.

Definition at line 128 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMaxTriesFactor(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ maxUIDMemory

int denoptim.programs.denovo.GAParameters.maxUIDMemory = 1000000

Maximum number of unique identifiers kept in memory.

Beyond this value the identifiers are dealt with using a file on disk.

Definition at line 363 of file GAParameters.java.

Referenced by denoptim.ga.EvolutionaryAlgorithm.EvolutionaryAlgorithm().

◆ maxXOverableSubGraphSize

int denoptim.programs.denovo.GAParameters.maxXOverableSubGraphSize = 20

Limit to the size of subgraphs that are exchanged during crossover.

Definition at line 408 of file GAParameters.java.

Referenced by denoptim.ga.Population.getXoverPartners(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.genetweeker.GeneOpsRunner.runXOver().

◆ minFitnessSD

double denoptim.programs.denovo.GAParameters.minFitnessSD = 0.000001

protected

Minimal standard deviation accepted in the fitness values of the initial population.

Definition at line 326 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMinFitnessSD().

◆ molGrowthMultiplier

double denoptim.programs.denovo.GAParameters.molGrowthMultiplier = 0.5

protected

Parameter controlling the molGrowth probability function of types 'EXP_DIFF' and 'TANH'.

Definition at line 195 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMolGrowthMultiplier(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ molGrowthProbabilityScheme

int denoptim.programs.denovo.GAParameters.molGrowthProbabilityScheme = 2

protected

Definition of the molGrowth probability function:

Definition at line 189 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMolGrowthProbabilityScheme(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ molGrowthSigmaMiddle

double denoptim.programs.denovo.GAParameters.molGrowthSigmaMiddle = 25

protected

Parameters controlling the molGrowth probability function of type 'SIGMA': level at which p=50% (can be a float)

Definition at line 207 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMolGrowthFactorMiddleSigma(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ molGrowthSigmaSteepness

double denoptim.programs.denovo.GAParameters.molGrowthSigmaSteepness = 0.2

protected

Parameters controlling the molGrowth probability function of type 'SIGMA': steepness of the function where p=50%.

Definition at line 201 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMolGrowthFactorSteepSigma(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ monitorDumpStep

int denoptim.programs.denovo.GAParameters.monitorDumpStep = 50

protected

Monitor dumps step.

The EA Monitor will dump data to file every this number of new attempts to generate candidate.

Definition at line 316 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMonitorDumpStep(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ monitorFile

String denoptim.programs.denovo.GAParameters.monitorFile = ""

private

Pathname of file where EA monitors dumps are printed.

Definition at line 91 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMonitorFile(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.setWorkingDirectory().

◆ mutatedGraphFailedEvalTolerant

boolean denoptim.programs.denovo.GAParameters.mutatedGraphFailedEvalTolerant = true

Flag that enables the ignoring of mutated graphs that lead to a failure in the evaluation of graphs that generates SMILES, InChI and molecular representation.

Definition at line 376 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParametersTest.testYesNoTrueFalseKeyword().

◆ mutationFailureTolerant

boolean denoptim.programs.denovo.GAParameters.mutationFailureTolerant = true

Flag that enables the ignoring of mutation events triggering exceptions.

Such events will still be recorded in the GA run Monitor.

Definition at line 396 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ mutationWeight

double denoptim.programs.denovo.GAParameters.mutationWeight = 1.0

protected

The relative weight at which mutation is performed.

Definition at line 242 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getMutationWeight(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ mutliSiteMutationWeights

double [] denoptim.programs.denovo.GAParameters.mutliSiteMutationWeights = new double[]{0,10,1}

private

The weights of multi-site mutations.

Definition at line 357 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getMultiSiteMutationWeights(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ numConvGen

int denoptim.programs.denovo.GAParameters.numConvGen = 5

protected

Number of identical generations before convergence is reached.

Definition at line 117 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getNumberOfConvergenceGenerations(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ numGenerations

int denoptim.programs.denovo.GAParameters.numGenerations = 100

protected

Maximum number of generations to run for.

Definition at line 122 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getNumberOfGenerations(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ numOfChildren

int denoptim.programs.denovo.GAParameters.numOfChildren = 5

protected

Number of children (i.e., new offspring) to be produced in each generation.

Definition at line 112 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getNumberOfChildren(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ numParallelTasks

int denoptim.programs.denovo.GAParameters.numParallelTasks = 0

protected

Maximum number of parallel tasks.

Definition at line 300 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getNumberOfCPU(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.processParameters().

◆ parallelizationScheme

int denoptim.programs.denovo.GAParameters.parallelizationScheme = 1

protected

Parallelization scheme: synchronous or asynchronous.

Definition at line 295 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getParallelizationScheme(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ parentsSurvive

boolean denoptim.programs.denovo.GAParameters.parentsSurvive = true

protected

Flag defining if population members can survive multiple generations (when this variable is true) or the population is refreshed at every generation (when this variable is false).

Definition at line 149 of file GAParameters.java.

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.parentsSurvive().

◆ populationSize

int denoptim.programs.denovo.GAParameters.populationSize = 50

protected

Size of the population.

Definition at line 106 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getPopulationSize(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.setPopulationSize().

◆ precisionLevel

int denoptim.programs.denovo.GAParameters.precisionLevel = 3

protected

Precision for reporting the value of the fitness.

Definition at line 310 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getPrecisionLevel(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ replacementStrategy

int denoptim.programs.denovo.GAParameters.replacementStrategy = 1

protected

Replacement strategy: 1) replace worst individuals with new ones that are better than the worst, 2) no replacement (the population keeps growing).

Obviously, with strategy 2 we consume a lot of resources.

Definition at line 141 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getReplacementStrategy(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ saveRingSystemsAsTemplatesNonScaff

boolean denoptim.programs.denovo.GAParameters.saveRingSystemsAsTemplatesNonScaff = false

protected

Flag controlling the possibility of collecting cyclic graph systems that do NOT include a scaffold and save them as new template non-scaffold building blocks.

Definition at line 344 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getSaveRingSystemsAsTemplatesNonScaff(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ saveRingSystemsAsTemplatesScaffolds

boolean denoptim.programs.denovo.GAParameters.saveRingSystemsAsTemplatesScaffolds = false

protected

Flag controlling the possibility of collecting cyclic graph systems that include a scaffold and save them as new template scaffolds.

Definition at line 337 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getSaveRingSystemsAsTemplatesScaff(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ saveRingSystemsFitnessThreshold

double denoptim.programs.denovo.GAParameters.saveRingSystemsFitnessThreshold = 0.10

protected

Fitness threshold for adding template to building block libraries.

This is expressed as percentage, i.e., if the fitness is in the best X% of the population, then the template is added to the scaffold/vertex library.

Definition at line 352 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getSaveRingSystemsFitnessThreshold(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ seed

long denoptim.programs.denovo.GAParameters.seed = 0L

protected

The seed value for random number generation.

Definition at line 290 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.processParameters().

◆ sortOrderDecreasing

boolean denoptim.programs.denovo.GAParameters.sortOrderDecreasing = true

protected

Flag controlling how to sort the population based on the fitness.

Definition at line 305 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.isSortOrderDecreasing().

◆ strXoverSelectionMode

String denoptim.programs.denovo.GAParameters.strXoverSelectionMode = xoverSelectionMode+""

protected

Crossover parents selection strategy: string.

Definition at line 270 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getSelectionStrategy(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ symmetricSubProbability

double denoptim.programs.denovo.GAParameters.symmetricSubProbability = 0.8

protected

The probability at which symmetric substitution occurs.

Definition at line 237 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.programs.denovo.GAParameters.getSymmetryProbability(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ timeStamp

String denoptim.programs.denovo.GAParameters.timeStamp = "NOTIMESTAMP"

Time stamp identifying this run.

Definition at line 50 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.createWorkingDirectory().

◆ uidFileIn

String denoptim.programs.denovo.GAParameters.uidFileIn = ""

protected

Pathname of the file with the list of individuals unique identifiers that are initially known.

Definition at line 80 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getUIDFileIn(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ uidFileOut

String denoptim.programs.denovo.GAParameters.uidFileOut = ""

protected

Pathname of the file where the individuals unique identifiers will be recorded.

Definition at line 86 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getUIDFileOut(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.setWorkingDirectory().

◆ uidMemoryOnDisk

String denoptim.programs.denovo.GAParameters.uidMemoryOnDisk = "memory_UIDs.txt"

Text file used to store unique identifiers beyond the limits of the memory (see GAParameters#maxUIDMemory).

Definition at line 369 of file GAParameters.java.

Referenced by denoptim.ga.EvolutionaryAlgorithm.EvolutionaryAlgorithm().

◆ useLevelBasedProb

boolean denoptim.programs.denovo.GAParameters.useLevelBasedProb = false

protected

Flag recording the intention to use level-controlled graph extension probability.

Definition at line 178 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.ga.EAUtils.getGrowthByLevelProbability(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.useLevelBasedProb().

◆ useMolSizeBasedProb

boolean denoptim.programs.denovo.GAParameters.useMolSizeBasedProb = false

protected

Flag recording the intention to use molecular size-controlled graph extension probability.

Definition at line 184 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.checkParameters(), denoptim.ga.EAUtils.getMolSizeProbability(), denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.useMolSizeBasedProb().

◆ visitedGraphsFile

String denoptim.programs.denovo.GAParameters.visitedGraphsFile = "GRAPHS.txt"

protected

Pathname to the file containing the list of previously visited graph.

Definition at line 101 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getVisitedGraphsFile().

◆ writePopOnDisk

boolean denoptim.programs.denovo.GAParameters.writePopOnDisk = false

protected

Flag requesting to write a SDF file that collects all the population members each time we report the population details on file.

Definition at line 414 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword(), and denoptim.programs.denovo.GAParameters.savePopFile().

◆ xoverFailureTolerant

boolean denoptim.programs.denovo.GAParameters.xoverFailureTolerant = true

Flag that enables the ignoring of crossover events triggering exceptions.

Such events will still be recorded in the GA run Monitor.

Definition at line 390 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ xoverGraphFailedEvalTolerant

boolean denoptim.programs.denovo.GAParameters.xoverGraphFailedEvalTolerant = true

Flag that enables the ignoring of crossover-ed graphs that lead to a f ailure in the evaluation of graphs that generates SMILES, InChI and molecular representation.

Definition at line 384 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.interpretKeyword().

◆ xoverSelectionMode

int denoptim.programs.denovo.GAParameters.xoverSelectionMode = 3

protected

Crossover parents selection strategy: integer code.

Definition at line 265 of file GAParameters.java.

Referenced by denoptim.programs.denovo.GAParameters.getSelectionStrategyType(), and denoptim.programs.denovo.GAParameters.interpretKeyword().

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

/github/workspace/src/main/java/denoptim/programs/denovo/GAParameters.java

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Attributes

Package Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GAParameters()

Member Function Documentation

◆ checkParameters()

◆ convertProbabilityScheme()

◆ coupleMutationAndCrossover()

◆ createWorkingDirectory()

◆ dumpMonitor()

◆ getConstructionWeight()

◆ getCrossoverWeight()

◆ getCrowdingFactorMiddleSigma()

◆ getCrowdingFactorSteepSigma()

◆ getCrowdingMultiplier()

◆ getCrowdingProbabilityScheme()

◆ getDataDirectory()

◆ getExcludedMutationTypes()

◆ getGrowthFactorMiddleSigma()

◆ getGrowthFactorSteepSigma()

◆ getGrowthMultiplier()

◆ getGrowthProbabilityScheme()

◆ getInitialPopulationFile()

◆ getInitMolsToFragmentFile()

◆ getInterfaceDir()

◆ getMaxGeneticOpAttempts()

◆ getMaxRingsAddedByMutation()

◆ getMaxTriesFactor()

◆ getMinFitnessSD()

◆ getMolGrowthFactorMiddleSigma()

◆ getMolGrowthFactorSteepSigma()

◆ getMolGrowthMultiplier()

◆ getMolGrowthProbabilityScheme()

◆ getMonitorDumpStep()

◆ getMonitorFile()

◆ getMultiSiteMutationWeights()

◆ getMutationWeight()

◆ getNumberOfChildren()

◆ getNumberOfConvergenceGenerations()

◆ getNumberOfCPU()

◆ getNumberOfGenerations()

◆ getParallelizationScheme()

◆ getPopulationSize()

◆ getPrecisionLevel()

◆ getPrintedList()

◆ getReplacementStrategy()

◆ getSaveRingSystemsAsTemplatesNonScaff()

◆ getSaveRingSystemsAsTemplatesScaff()

◆ getSaveRingSystemsFitnessThreshold()

◆ getSelectionStrategy()

◆ getSelectionStrategyType()

◆ getSymmetryProbability()

◆ getUIDFileIn()

◆ getUIDFileOut()

◆ getVisitedGraphsFile()

◆ interpretKeyword()

◆ isSortOrderDecreasing()

◆ keepBestSibling()

◆ maxOffsprintFromXover()

◆ parentsSurvive()

◆ processParameters()

◆ savePopFile()

◆ setPopulationSize()

◆ setWorkingDirectory()

◆ useLevelBasedProb()

◆ useMolSizeBasedProb()

Member Data Documentation

◆ buildAnewFailureTolerant

◆ builtAnewWeight

◆ coupleMutationAndCrossover

◆ crossoverWeight

◆ crowdingMultiplier

◆ crowdingProbabilityScheme