denoptim.programs.moldecularmodelbuilder.MMBuilderParameters Member List

This is the complete list of members for denoptim.programs.moldecularmodelbuilder.MMBuilderParameters, including all inherited members.

atomOrderingScheme	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
checkOtherParameters()	denoptim.programs.RunTimeParameters	protected
checkParameters()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
containsParameters(ParametersType type)	denoptim.programs.RunTimeParameters
debug	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
debug()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
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
forceFieldFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
getAtomOrderingScheme()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getInitPSSROTParams()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getInputSDFFile()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getInstanceFor(ParametersType paramType)	denoptim.programs.RunTimeParameters	privatestatic
getINTXYZTool()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getKeepDummyFlag()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getKeyFileParams()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getLogFilePathname()	denoptim.programs.RunTimeParameters
getLogger()	denoptim.programs.RunTimeParameters
getOutputSDFFile()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getParameters(ParametersType type)	denoptim.programs.RunTimeParameters
getParamFile()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getPrintedList()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getPSSROTTool()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRandomizer()	denoptim.programs.RunTimeParameters
getRandomSeed()	denoptim.programs.RunTimeParameters
getRestPSSROTParams()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRSInitPSSROTParams()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRSKeyFileParams()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getRSRestPSSROTParams()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getTaskID()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getTinkerMap()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getVerbosity()	denoptim.programs.RunTimeParameters
getWorkDirectory()	denoptim.programs.RunTimeParameters
getWorkingDirectory()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
getXYZINTTool()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
inpSDFFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
interpretKeyword(String key, String value)	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
denoptim::programs::RunTimeParameters.interpretKeyword(String line)	denoptim.programs.RunTimeParameters
isMaster	denoptim.programs.RunTimeParameters	protected
keepDummy	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
keyFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
keyFileParams	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
logFile	denoptim.programs.RunTimeParameters	protected
logger	denoptim.programs.RunTimeParameters	private
MMBuilderParameters()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
NL	denoptim.programs.RunTimeParameters
otherParameters	denoptim.programs.RunTimeParameters	protected
outSDFFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
paramType	denoptim.programs.RunTimeParameters	private
paramTypeName()	denoptim.programs.RunTimeParameters
printParameters()	denoptim.programs.RunTimeParameters
processOtherParameters()	denoptim.programs.RunTimeParameters	protected
processParameters()	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters
pssrotFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
pssrotParams_Init	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
pssrotParams_Rest	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
readParameterFile(String infile)	denoptim.programs.RunTimeParameters
readParameterLine(String line)	denoptim.programs.RunTimeParameters
readYesNoTrueFalse(String s)	denoptim.programs.RunTimeParameters	static
rng	denoptim.programs.RunTimeParameters	private
rsKeyFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
rsKeyFileParams	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
rsPssrotFile	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
rsPssrotParams_Init	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
rsPssrotParams_Rest	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
RunTimeParameters(ParametersType paramType)	denoptim.programs.RunTimeParameters
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
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
taskID	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
TINKER_MAP	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
toolINTXYZ	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
toolPSSROT	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
toolXYZINT	denoptim.programs.moldecularmodelbuilder.MMBuilderParameters	protected
verbosity	denoptim.programs.RunTimeParameters	protected
verbosityTologLevel()	denoptim.programs.RunTimeParameters	private
workDir	denoptim.programs.RunTimeParameters	protected