This is the complete list of members for denoptim.ga.EAUtils, including all inherited members.

apPairsAreOverlapping(Iterable< RelatedAPPair > pairs)	denoptim.ga.EAUtils	static
appendVertexesToGraphFollowingEdges(DGraph graph, AtomicInteger vId, List< Vertex > vertexes)	denoptim.ga.EAUtils	privatestatic
buildCandidateByFragmentingMolecule(IAtomContainer mol, Monitor mnt, GAParameters settings, int index)	denoptim.ga.EAUtils	static
buildCandidateByMutation(List< Candidate > eligibleParents, Monitor mnt, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
buildCandidateByXOver(List< Candidate > eligibleParents, Population population, Monitor mnt, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
buildCandidateByXOver(List< Candidate > eligibleParents, Population population, Monitor mnt, int[] choiceOfParents, int choiceOfXOverSites, int choiceOfOffstring, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
buildCandidateFromScratch(Monitor mnt, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
buildCandidatesByXOver(List< Candidate > eligibleParents, Population population, Monitor mnt, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
buildCandidatesByXOver(List< Candidate > eligibleParents, Population population, Monitor mnt, int[] choiceOfParents, int choiceOfXOverSites, int choiceOfOffstring, GAParameters settings, int maxCandidatesToReturn)	denoptim.ga.EAUtils	protectedstatic
buildGraph(GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
canBeUsedForRingFusion(AttachmentPoint ap, Set< Long > originalVertexIDs, FragmentSpace fs)	denoptim.ga.EAUtils	privatestatic
chooseGenerationMethod(GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
chooseNumberOfSitesToMutate(double[] multiSiteMutationProb, double hit)	denoptim.ga.EAUtils	static
combineRelatedAPPair(List< RelatedAPPair > pool, int k, int limit)	denoptim.ga.EAUtils	privatestatic
combineRelatedAPPairUtil(List< RelatedAPPair > pool, int left, int k, List< RelatedAPPair > tmp, List< List< RelatedAPPair > > allCombs, int limit)	denoptim.ga.EAUtils	privatestatic
containsMolecule(Population mols, String molcode)	denoptim.ga.EAUtils	protectedstatic
createFolderForGeneration(int genId, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
df	denoptim.ga.EAUtils	privatestatic
enUsLocale	denoptim.ga.EAUtils	privatestatic
foundForbiddenEnd(DGraph molGraph, FragmentSpaceParameters fsParams)	denoptim.ga.EAUtils	protectedstatic
fragmentPool	denoptim.ga.EAUtils	protectedstatic
FSEP	denoptim.ga.EAUtils	privatestatic
getCrowdedness(AttachmentPoint ap)	denoptim.ga.EAUtils	static
getCrowdedness(AttachmentPoint ap, boolean ignoreFreeRCVs)	denoptim.ga.EAUtils	static
getCrowdingProbability(AttachmentPoint ap, GAParameters settings)	denoptim.ga.EAUtils	static
getCrowdingProbability(int crowdedness, GAParameters settings)	denoptim.ga.EAUtils	static
getCrowdingProbability(AttachmentPoint ap, int scheme, double lambda, double sigmaOne, double sigmaTwo)	denoptim.ga.EAUtils	static
getCrowdingProbabilityForCrowdedness(int crowdedness, int scheme, double lambda, double sigmaOne, double sigmaTwo)	denoptim.ga.EAUtils	static
getFitnesses(Population mols)	denoptim.ga.EAUtils	protectedstatic
getGrowthByLevelProbability(int level, GAParameters settings)	denoptim.ga.EAUtils	static
getGrowthProbabilityAtLevel(int level, int scheme, double lambda, double sigmaOne, double sigmaTwo)	denoptim.ga.EAUtils	static
getMolSizeProbability(DGraph graph, GAParameters settings)	denoptim.ga.EAUtils	static
getMolSizeProbability(DGraph graph, int scheme, double lambda, double sigmaOne, double sigmaTwo)	denoptim.ga.EAUtils	static
getPathNameToFinalPopulationDetailsFile(GAParameters settings)	denoptim.ga.EAUtils	static
getPathNameToFinalPopulationFolder(GAParameters settings)	denoptim.ga.EAUtils	static
getPathNameToGenerationDetailsFile(int genID, GAParameters settings)	denoptim.ga.EAUtils	static
getPathNameToGenerationFolder(int genID, GAParameters settings)	denoptim.ga.EAUtils	static
getPopulationFromFile(String filename, Population population, SizeControlledSet uniqueIDsSet, String genDir, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
getPopulationSD(Population molPopulation)	denoptim.ga.EAUtils	protectedstatic
getProbability(double value, int scheme, double lambda, double sigmaOne, double sigmaTwo)	denoptim.ga.EAUtils	static
getSummaryStatistics(Population popln, GAParameters settings)	denoptim.ga.EAUtils	privatestatic
getUsableAliphaticBridges(APClass apcA, APClass apcB, int[] allowedLengths, FragmentSpace fragSpace)	denoptim.ga.EAUtils	static
getUsableAromaticBridges(String elInIncomingFrag, int[] allowedLengths, FragmentSpace fragSpace)	denoptim.ga.EAUtils	static
importInitialPopulation(SizeControlledSet uniqueIDsSet, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
initialiseFormatter()	denoptim.ga.EAUtils	privatestatic
lstFragmentClass	denoptim.ga.EAUtils	protectedstatic
makeGraphFromFragmentationOfMol(IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy)	denoptim.ga.EAUtils	static
makeGraphFromFragmentationOfMol(IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy, double linearAngleLimit)	denoptim.ga.EAUtils	static
makeGraphFromFragmentationOfMol(IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy, FragmentSpace fragSpace)	denoptim.ga.EAUtils	static
makeGraphFromFragmentationOfMol(IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy, double linearAngleLimit, FragmentSpace fragSpace)	denoptim.ga.EAUtils	static
makeGraphFromFragmentationOfMol(IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy, double linearAngleLimit, boolean embedRingsInTemplates, ContractLevel ringTmplContract, FragmentSpace fragSpace, Monitor monitor)	denoptim.ga.EAUtils	static
NL	denoptim.ga.EAUtils	privatestatic
outputFinalResults(Population popln, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
outputPopulationDetails(Population population, String filename, GAParameters settings, boolean printpathNames)	denoptim.ga.EAUtils	static
performFBCC(List< Candidate > eligibleParents, Population population, int[] choiceOfParents, int choiceOfXOverSites, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
pickNewCandidateGenerationMode(double xoverWeight, double mutWeight, double newWeight, Randomizer randomizer)	denoptim.ga.EAUtils	static
readCandidateFromFile(File srcFile, Monitor mnt, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
readUID(String infile, HashSet< String > lstInchi)	denoptim.ga.EAUtils	protectedstatic
searchRingFusionSites(DGraph graph, GAParameters gaParams)	denoptim.ga.EAUtils	static
searchRingFusionSites(DGraph graph, FragmentSpace fragSpace, RingClosureParameters rcParams, boolean projectOnSymmetricAPs, Logger logger, Randomizer rng)	denoptim.ga.EAUtils	static
selectBasedOnFitness(List< Candidate > eligibleParents, int number, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
selectNonScaffoldNonCapVertex(DGraph g, Randomizer randomizer)	denoptim.ga.EAUtils	protectedstatic
setupRings(Object[] res, DGraph molGraph, GAParameters settings)	denoptim.ga.EAUtils	protectedstatic
setVertexCounterValue(Population population)	denoptim.ga.EAUtils	protectedstatic
shareAPs(RelatedAPPair pairA, Iterable< RelatedAPPair > lstB)	denoptim.ga.EAUtils	static
storePairsSymmetricRelations(RelatedAPPair pair, SymmetricAPs symAPs, Map< SymmetricSetWithMode, List< RelatedAPPair > > storage)	denoptim.ga.EAUtils	privatestatic
writeUID(String outfile, HashSet< String > lstInchi, boolean append)	denoptim.ga.EAUtils	protectedstatic