denoptim.programs.fragmenter.FragmenterParameters Member List

This is the complete list of members for denoptim.programs.fragmenter.FragmenterParameters, including all inherited members.

acceptUnsetToSingeBO()	denoptim.programs.fragmenter.FragmenterParameters
acceptUnsetToSingeBOApprox	denoptim.programs.fragmenter.FragmenterParameters	private
addExplicitH	denoptim.programs.fragmenter.FragmenterParameters	private
addExplicitH()	denoptim.programs.fragmenter.FragmenterParameters
checkFormula	denoptim.programs.fragmenter.FragmenterParameters	private
checkOtherParameters()	denoptim.programs.RunTimeParameters	protected
checkParameters()	denoptim.programs.fragmenter.FragmenterParameters
containsParameters(ParametersType type)	denoptim.programs.RunTimeParameters
createWorkingDirectory()	denoptim.programs.fragmenter.FragmenterParameters	private
cutRulesFile	denoptim.programs.fragmenter.FragmenterParameters	private
cuttingRules	denoptim.programs.fragmenter.FragmenterParameters	package
doAddDuOnLinearity	denoptim.programs.fragmenter.FragmenterParameters	private
doAddDuOnLinearity()	denoptim.programs.fragmenter.FragmenterParameters
doCheckFormula()	denoptim.programs.fragmenter.FragmenterParameters
doExtactRepresentativeConformer	denoptim.programs.fragmenter.FragmenterParameters	private
doExtactRepresentativeConformer()	denoptim.programs.fragmenter.FragmenterParameters
doFiltering	denoptim.programs.fragmenter.FragmenterParameters	private
doFiltering()	denoptim.programs.fragmenter.FragmenterParameters
doFragmentation	denoptim.programs.fragmenter.FragmenterParameters	private
doFragmentation()	denoptim.programs.fragmenter.FragmenterParameters
doManageIsomorphicFamilies	denoptim.programs.fragmenter.FragmenterParameters	private
doManageIsomorphicFamilies()	denoptim.programs.fragmenter.FragmenterParameters
doPreFilter()	denoptim.programs.fragmenter.FragmenterParameters
doRejectWeirdIsotopes	denoptim.programs.fragmenter.FragmenterParameters	private
doRejectWeirdIsotopes()	denoptim.programs.fragmenter.FragmenterParameters
embeddedRingsContract	denoptim.programs.fragmenter.FragmenterParameters	protected
embedRingsInTemplate	denoptim.programs.fragmenter.FragmenterParameters	protected
embedRingsInTemplate()	denoptim.programs.fragmenter.FragmenterParameters
ensureFileExists(String pathname)	denoptim.programs.RunTimeParameters	protected
ensureFileExistsIfSet(String pathname)	denoptim.programs.RunTimeParameters	protected
ensureInRange(String paramName, int value, int min, int max, String paramKey)	denoptim.programs.RunTimeParameters	protected
ensureIsPositive(String paramName, int value, String paramKey)	denoptim.programs.RunTimeParameters	protected
ensureIsPositiveOrZero(String paramName, int value, String paramKey)	denoptim.programs.RunTimeParameters	protected
ensureNotNull(String paramName, String param, String paramKey)	denoptim.programs.RunTimeParameters	protected
factorForSDOnStatsOfUnimodalPop	denoptim.programs.fragmenter.FragmenterParameters	private
formulaCriteriaLessThan	denoptim.programs.fragmenter.FragmenterParameters	private
formulaCriteriaMoreThan	denoptim.programs.fragmenter.FragmenterParameters	private
formulae	denoptim.programs.fragmenter.FragmenterParameters	private
formulaeFile	denoptim.programs.fragmenter.FragmenterParameters	private
FragmenterParameters()	denoptim.programs.fragmenter.FragmenterParameters
fragRejectionSMARTS	denoptim.programs.fragmenter.FragmenterParameters	private
fragRetentionSMARTS	denoptim.programs.fragmenter.FragmenterParameters	private
getCuttingRules()	denoptim.programs.fragmenter.FragmenterParameters
getCuttingRulesFilePathname()	denoptim.programs.fragmenter.FragmenterParameters
getEmbeddedRingsContract()	denoptim.programs.fragmenter.FragmenterParameters
getFactorForSDOnStatsOfUnimodalPop()	denoptim.programs.fragmenter.FragmenterParameters
getFormulae()	denoptim.programs.fragmenter.FragmenterParameters
getFormulaeFile()	denoptim.programs.fragmenter.FragmenterParameters
getFragRejectionSMARTS()	denoptim.programs.fragmenter.FragmenterParameters
getFragRetentionSMARTS()	denoptim.programs.fragmenter.FragmenterParameters
getIgnorableFragments()	denoptim.programs.fragmenter.FragmenterParameters
getInstanceFor(ParametersType paramType)	denoptim.programs.RunTimeParameters	privatestatic
getIsomorphicSampleSize()	denoptim.programs.fragmenter.FragmenterParameters
getIsomorphsCount()	denoptim.programs.fragmenter.FragmenterParameters
getLinearAngleLimit()	denoptim.programs.fragmenter.FragmenterParameters
getLogFilePathname()	denoptim.programs.RunTimeParameters
getLogger()	denoptim.programs.RunTimeParameters
getMaxFragHeavyAtomCount()	denoptim.programs.fragmenter.FragmenterParameters
getMaxNoiseUnimodalPop()	denoptim.programs.fragmenter.FragmenterParameters
getMinFragHeavyAtomCount()	denoptim.programs.fragmenter.FragmenterParameters
getMWSlotFileNameAllFrags(String mwSlotId)	denoptim.programs.fragmenter.FragmenterParameters
getMWSlotFileNameUnqFrags(String mwSlotId)	denoptim.programs.fragmenter.FragmenterParameters
getMWSlotSize()	denoptim.programs.fragmenter.FragmenterParameters
getMWSlotToAllFragsFile()	denoptim.programs.fragmenter.FragmenterParameters
getMWSlotToUnqFragsFile()	denoptim.programs.fragmenter.FragmenterParameters
getNumTasks()	denoptim.programs.fragmenter.FragmenterParameters
getParameters(ParametersType type)	denoptim.programs.RunTimeParameters
getPreFiltrationSMARTS()	denoptim.programs.fragmenter.FragmenterParameters
getPrintedList()	denoptim.programs.fragmenter.FragmenterParameters
getRandomizer()	denoptim.programs.RunTimeParameters
getRandomSeed()	denoptim.programs.RunTimeParameters
getRejectedAPClassCombinations()	denoptim.programs.fragmenter.FragmenterParameters
getRejectedAPClasses()	denoptim.programs.fragmenter.FragmenterParameters
getRejectedElements()	denoptim.programs.fragmenter.FragmenterParameters
getRejectedFormulaLessThan()	denoptim.programs.fragmenter.FragmenterParameters
getRejectedFormulaMoreThan()	denoptim.programs.fragmenter.FragmenterParameters
getScaffoldingPolicy()	denoptim.programs.fragmenter.FragmenterParameters
getSizeUnimodalPop()	denoptim.programs.fragmenter.FragmenterParameters
getStructuresFile()	denoptim.programs.fragmenter.FragmenterParameters
getTargetFragments()	denoptim.programs.fragmenter.FragmenterParameters
getVerbosity()	denoptim.programs.RunTimeParameters
getWorkDirectory()	denoptim.programs.RunTimeParameters
ignorableFragments	denoptim.programs.fragmenter.FragmenterParameters	private
ignorableFragmentsFile	denoptim.programs.fragmenter.FragmenterParameters	private
interpretKeyword(String key, String value)	denoptim.programs.fragmenter.FragmenterParameters
denoptim::programs::RunTimeParameters.interpretKeyword(String line)	denoptim.programs.RunTimeParameters
isMaster	denoptim.programs.RunTimeParameters	protected
isomorphicSampleSize	denoptim.programs.fragmenter.FragmenterParameters	private
isomorphsCount	denoptim.programs.fragmenter.FragmenterParameters	private
isSaveClustersOfConformerToFile()	denoptim.programs.fragmenter.FragmenterParameters
isStandaloneFragmentClustering	denoptim.programs.fragmenter.FragmenterParameters	private
isStandaloneFragmentClustering()	denoptim.programs.fragmenter.FragmenterParameters
isUseCentroidsAsRepresentativeConformer()	denoptim.programs.fragmenter.FragmenterParameters
isWorkingIn3D()	denoptim.programs.fragmenter.FragmenterParameters
linearAngleLimit	denoptim.programs.fragmenter.FragmenterParameters	private
logFile	denoptim.programs.RunTimeParameters	protected
logger	denoptim.programs.RunTimeParameters	private
MANAGEMWSLOTSSLOCK	denoptim.programs.fragmenter.FragmenterParameters
maxFragHeavyAtomCount	denoptim.programs.fragmenter.FragmenterParameters	private
MAXISOMORPHICSAMPLESIZE	denoptim.programs.fragmenter.FragmenterParameters	static
maxNoiseUnimodalPop	denoptim.programs.fragmenter.FragmenterParameters	private
minFragHeavyAtomCount	denoptim.programs.fragmenter.FragmenterParameters	private
mwSlotSize	denoptim.programs.fragmenter.FragmenterParameters	private
mwSlotToAllFragsFile	denoptim.programs.fragmenter.FragmenterParameters	private
mwSlotToUnqFragsFile	denoptim.programs.fragmenter.FragmenterParameters	private
newIsomorphicFamilyID()	denoptim.programs.fragmenter.FragmenterParameters
NL	denoptim.programs.RunTimeParameters
numParallelTasks	denoptim.programs.fragmenter.FragmenterParameters	private
otherParameters	denoptim.programs.RunTimeParameters	protected
paramType	denoptim.programs.RunTimeParameters	private
paramTypeName()	denoptim.programs.RunTimeParameters
preFilter	denoptim.programs.fragmenter.FragmenterParameters	private
preFilterSMARTS	denoptim.programs.fragmenter.FragmenterParameters	private
printParameters()	denoptim.programs.RunTimeParameters
processOtherParameters()	denoptim.programs.RunTimeParameters	protected
processParameters()	denoptim.programs.fragmenter.FragmenterParameters
readParameterFile(String infile)	denoptim.programs.RunTimeParameters
readParameterLine(String line)	denoptim.programs.RunTimeParameters
readYesNoTrueFalse(String s)	denoptim.programs.RunTimeParameters	static
rejectedAPClassCombinations	denoptim.programs.fragmenter.FragmenterParameters	private
rejectedAPClasses	denoptim.programs.fragmenter.FragmenterParameters	private
rejectedElements	denoptim.programs.fragmenter.FragmenterParameters	private
rng	denoptim.programs.RunTimeParameters	private
RunTimeParameters(ParametersType paramType)	denoptim.programs.RunTimeParameters
saveClustersOfConformerToFile	denoptim.programs.fragmenter.FragmenterParameters	private
scaffoldingPolicy	denoptim.programs.fragmenter.FragmenterParameters	private
setCheckFormula(boolean checkFormula)	denoptim.programs.fragmenter.FragmenterParameters
setCuttingRules(List< CuttingRule > cuttingRules)	denoptim.programs.fragmenter.FragmenterParameters
setCuttingRulesFilePathname(String pathname)	denoptim.programs.fragmenter.FragmenterParameters
setEmbeddedRingsContract(ContractLevel embeddedRingsContract)	denoptim.programs.fragmenter.FragmenterParameters
setEmbedRingsInTemplate(boolean embedRingsInTemplate)	denoptim.programs.fragmenter.FragmenterParameters
setFactorForSDOnStatsOfUnimodalPop(double factorForSDOnStatsOfUnimodalPop)	denoptim.programs.fragmenter.FragmenterParameters
setFormulaeFile(String formulaeFile)	denoptim.programs.fragmenter.FragmenterParameters
setFragRejectionSMARTS(Map< String, String > fragRejectionSMARTS)	denoptim.programs.fragmenter.FragmenterParameters
setFragRetentionSMARTS(Map< String, String > fragRetentionSMARTS)	denoptim.programs.fragmenter.FragmenterParameters
setIsomorphicSampleSize(int isomorphicSampleSize)	denoptim.programs.fragmenter.FragmenterParameters
setLinearAngleLimit(double linearAngleLimit)	denoptim.programs.fragmenter.FragmenterParameters
setLogFilePathname(String pathname)	denoptim.programs.RunTimeParameters
setLogger(Logger logger)	denoptim.programs.RunTimeParameters	private
setMaxFragHeavyAtomCount(int maxFragHeavyAtomCount)	denoptim.programs.fragmenter.FragmenterParameters
setMaxNoiseUnimodalPop(double maxNoiseUnimodalPop)	denoptim.programs.fragmenter.FragmenterParameters
setMinFragHeavyAtomCount(int minFragHeavyAtomCount)	denoptim.programs.fragmenter.FragmenterParameters
setMWSlotSize(int mwSlotSize)	denoptim.programs.fragmenter.FragmenterParameters
setMWSlotToAllFragsFile(Map< String, File > mwSlotToAllFragsFile)	denoptim.programs.fragmenter.FragmenterParameters
setNumTasks(int numParallelTasks)	denoptim.programs.fragmenter.FragmenterParameters
setParameters(RunTimeParameters otherParams)	denoptim.programs.RunTimeParameters
setRandomizer(Randomizer rng)	denoptim.programs.RunTimeParameters
setRejectedAPClassCombinations(Set< String[]> rejectedAPClassCombinations)	denoptim.programs.fragmenter.FragmenterParameters
setRejectedAPClasses(Set< String > rejectedAPClasses)	denoptim.programs.fragmenter.FragmenterParameters
setRejectedElements(Set< String > rejectedElements)	denoptim.programs.fragmenter.FragmenterParameters
setRejectedFormulaLessThan(Map< String, Double > formulaMax)	denoptim.programs.fragmenter.FragmenterParameters
setRejectedFormulaMoreThan(Set< Map< String, Double > > formulaCriteriaMoreThan)	denoptim.programs.fragmenter.FragmenterParameters
setRejectWeirdIsotopes(boolean doRejectWeirdIsotopes)	denoptim.programs.fragmenter.FragmenterParameters
setSaveClustersOfConformerToFile(boolean saveClustersOfConformerToFile)	denoptim.programs.fragmenter.FragmenterParameters
setScaffoldingPolicy(ScaffoldingPolicy sp)	denoptim.programs.fragmenter.FragmenterParameters
setSizeUnimodalPop(int sizeUnimodalPop)	denoptim.programs.fragmenter.FragmenterParameters
setStructuresFile(String structuresFile)	denoptim.programs.fragmenter.FragmenterParameters
setUseCentroidsAsRepresentativeConformer(boolean useCentroidsAsRepresentativeConformer)	denoptim.programs.fragmenter.FragmenterParameters
setVerbosity(int l)	denoptim.programs.RunTimeParameters
setWorkDirectory(String pathname)	denoptim.programs.RunTimeParameters
setWorkingIn3D(boolean workingIn3D)	denoptim.programs.fragmenter.FragmenterParameters
sizeUnimodalPop	denoptim.programs.fragmenter.FragmenterParameters	private
startConsoleLogger(String loggerIdentifier)	denoptim.programs.RunTimeParameters
startProgramSpecificLogger(String loggerIdentifier)	denoptim.programs.RunTimeParameters
startProgramSpecificLogger(String loggerIdentifier, boolean toLogFile)	denoptim.programs.RunTimeParameters
startRandomizer()	denoptim.programs.RunTimeParameters
startRandomizer(long seed)	denoptim.programs.RunTimeParameters
structuresFile	denoptim.programs.fragmenter.FragmenterParameters	private
targetFragments	denoptim.programs.fragmenter.FragmenterParameters	private
targetFragmentsFile	denoptim.programs.fragmenter.FragmenterParameters	private
unqIsomorphicFamilyId	denoptim.programs.fragmenter.FragmenterParameters	private
useCentroidsAsRepresentativeConformer	denoptim.programs.fragmenter.FragmenterParameters	private
verbosity	denoptim.programs.RunTimeParameters	protected
verbosityTologLevel()	denoptim.programs.RunTimeParameters	private
workDir	denoptim.programs.RunTimeParameters	protected
workingIn3D	denoptim.programs.fragmenter.FragmenterParameters	private