denoptim.graph.rings.RingClosureParameters Member List

This is the complete list of members for denoptim.graph.rings.RingClosureParameters, including all inherited members.

allowRingClosures(boolean value)	denoptim.graph.rings.RingClosureParameters
allowRingClosures()	denoptim.graph.rings.RingClosureParameters
bridgeHeadFindingRules	denoptim.graph.rings.RingClosureParameters	protected
buildChelatesMode	denoptim.graph.rings.RingClosureParameters	protected
buildChelatesMode()	denoptim.graph.rings.RingClosureParameters
checkInterdependentChains()	denoptim.graph.rings.RingClosureParameters
checkInterdepPaths	denoptim.graph.rings.RingClosureParameters	protected
checkOtherParameters()	denoptim.programs.RunTimeParameters	protected
checkParameters()	denoptim.graph.rings.RingClosureParameters
closeRings	denoptim.graph.rings.RingClosureParameters	protected
containsParameters(ParametersType type)	denoptim.programs.RunTimeParameters
doExhaustiveConfSrch()	denoptim.graph.rings.RingClosureParameters
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
exhaustiveConfSrch	denoptim.graph.rings.RingClosureParameters	protected
getBridgeHeadFindingRules()	denoptim.graph.rings.RingClosureParameters
getClosabilityEvalMode()	denoptim.graph.rings.RingClosureParameters
getConfPathExtraTolerance()	denoptim.graph.rings.RingClosureParameters
getConstitutionalClosabilityConds()	denoptim.graph.rings.RingClosureParameters
getInstanceFor(ParametersType paramType)	denoptim.programs.RunTimeParameters	privatestatic
getLinearityLimit()	denoptim.graph.rings.RingClosureParameters
getLogFilePathname()	denoptim.programs.RunTimeParameters
getLogger()	denoptim.programs.RunTimeParameters
getMaxNumberRotatableBonds()	denoptim.graph.rings.RingClosureParameters
getMaxRcaPerType(String type)	denoptim.graph.rings.RingClosureParameters
getMaxRingClosures()	denoptim.graph.rings.RingClosureParameters
getMaxRingSize()	denoptim.graph.rings.RingClosureParameters
getMinRcaPerType(String type)	denoptim.graph.rings.RingClosureParameters
getMinRingClosures()	denoptim.graph.rings.RingClosureParameters
getParameters(ParametersType type)	denoptim.programs.RunTimeParameters
getPathConfSearchStep()	denoptim.graph.rings.RingClosureParameters
getPrintedList()	denoptim.graph.rings.RingClosureParameters
getRandomizer()	denoptim.programs.RunTimeParameters
getRandomSeed()	denoptim.programs.RunTimeParameters
getRCCLibraryFolder()	denoptim.graph.rings.RingClosureParameters
getRCCLibraryIndexFile()	denoptim.graph.rings.RingClosureParameters
getRCDistTolerance()	denoptim.graph.rings.RingClosureParameters
getRCDotPrTolerance()	denoptim.graph.rings.RingClosureParameters
getRequiredRingElements()	denoptim.graph.rings.RingClosureParameters
getRingClosuresArchive()	denoptim.graph.rings.RingClosureParameters
getRingSizeBias()	denoptim.graph.rings.RingClosureParameters
getVerbosity()	denoptim.graph.rings.RingClosureParameters
getWorkDirectory()	denoptim.programs.RunTimeParameters
interpretKeyword(String key, String value)	denoptim.graph.rings.RingClosureParameters
denoptim::programs::RunTimeParameters.interpretKeyword(String line)	denoptim.programs.RunTimeParameters
isMaster	denoptim.programs.RunTimeParameters	protected
linearityLimit	denoptim.graph.rings.RingClosureParameters	protected
logFile	denoptim.programs.RunTimeParameters	protected
logger	denoptim.programs.RunTimeParameters	private
maxRcaPerType	denoptim.graph.rings.RingClosureParameters	protected
maxRingClosures	denoptim.graph.rings.RingClosureParameters	protected
maxRingSize	denoptim.graph.rings.RingClosureParameters	protected
maxRotBonds	denoptim.graph.rings.RingClosureParameters	protected
metalCoordinatingAPClasses	denoptim.graph.rings.RingClosureParameters	protected
minRcaPerType	denoptim.graph.rings.RingClosureParameters	protected
minRingClosures	denoptim.graph.rings.RingClosureParameters	protected
NL	denoptim.programs.RunTimeParameters
otherParameters	denoptim.programs.RunTimeParameters	protected
paramType	denoptim.programs.RunTimeParameters	private
paramTypeName()	denoptim.programs.RunTimeParameters
pathConfSearchExtraTol	denoptim.graph.rings.RingClosureParameters	protected
pathConfSearchStep	denoptim.graph.rings.RingClosureParameters	protected
printParameters()	denoptim.programs.RunTimeParameters
processOtherParameters()	denoptim.programs.RunTimeParameters	protected
processParameters()	denoptim.graph.rings.RingClosureParameters
rcArchive	denoptim.graph.rings.RingClosureParameters	private
rccFolder	denoptim.graph.rings.RingClosureParameters	protected
rccIndex	denoptim.graph.rings.RingClosureParameters	protected
rceMode	denoptim.graph.rings.RingClosureParameters	protected
rcMaxDot	denoptim.graph.rings.RingClosureParameters	protected
rcTolDist	denoptim.graph.rings.RingClosureParameters	protected
readParameterFile(String infile)	denoptim.programs.RunTimeParameters
readParameterLine(String line)	denoptim.programs.RunTimeParameters
readYesNoTrueFalse(String s)	denoptim.programs.RunTimeParameters	static
reqElInRings	denoptim.graph.rings.RingClosureParameters	protected
requireCompleteRingclosure	denoptim.graph.rings.RingClosureParameters
ringClosabCondAsSMARTS	denoptim.graph.rings.RingClosureParameters	protected
RingClosureParameters()	denoptim.graph.rings.RingClosureParameters
ringSizeBias	denoptim.graph.rings.RingClosureParameters	protected
rng	denoptim.programs.RunTimeParameters	private
RunTimeParameters(ParametersType paramType)	denoptim.programs.RunTimeParameters
selectFragmentsFromClosableChains()	denoptim.graph.rings.RingClosureParameters
selectFragsFromCC	denoptim.graph.rings.RingClosureParameters	protected
serializeRCCs	denoptim.graph.rings.RingClosureParameters	protected
serializeRCCs()	denoptim.graph.rings.RingClosureParameters
setConstitutionalClosabilityConds(Map< String, String > ringClosabCondAsSMARTS)	denoptim.graph.rings.RingClosureParameters
setLogFilePathname(String pathname)	denoptim.programs.RunTimeParameters
setLogger(Logger logger)	denoptim.programs.RunTimeParameters	private
setParameters(RunTimeParameters otherParams)	denoptim.programs.RunTimeParameters
setRandomizer(Randomizer rng)	denoptim.programs.RunTimeParameters
setRingSizeBias(List< Integer > biases)	denoptim.graph.rings.RingClosureParameters
setVerbosity(int l)	denoptim.programs.RunTimeParameters
setWorkDirectory(String pathname)	denoptim.programs.RunTimeParameters
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
verbosity	denoptim.programs.RunTimeParameters	protected
verbosityTologLevel()	denoptim.programs.RunTimeParameters	private
workDir	denoptim.programs.RunTimeParameters	protected