Parameters controlling execution of GraphEditor. More...

Inheritance diagram for denoptim.programs.mol2graph.Mol2GraphParameters:

Collaboration diagram for denoptim.programs.mol2graph.Mol2GraphParameters:

Public Member Functions
	Mol2GraphParameters ()
	Constructor. More...

int	getInputMolsCount ()

IAtomContainer	getInputMol (int i)

String	getOutFile ()

FileFormat	getOutFormat ()

List< CuttingRule >	getCuttingRules ()

ScaffoldingPolicy	getScaffoldingPolicy ()

double	getLinearAngleLimit ()

FragmentSpace	getFragmentSpace ()

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

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

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

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

Private Member Functions
void	ensureFragmenterParams ()

void	ensureFragSpareParams ()

Private Attributes
String	inFile
	File with input graphs. More...

List< IAtomContainer >	inMols
	Input molecular objects. More...

String	outGraphsFile = null
	File with output graphs. More...

FileFormat	outGraphsFormat = FileFormat.GRAPHSDF

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

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...

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...

Detailed Description

Parameters controlling execution of GraphEditor.

Author: Marco Foscato

Definition at line 48 of file Mol2GraphParameters.java.

Constructor & Destructor Documentation

◆ Mol2GraphParameters()

denoptim.programs.mol2graph.Mol2GraphParameters.Mol2GraphParameters ( )

Constructor.

Definition at line 71 of file Mol2GraphParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.M2G_PARAMS.

Member Function Documentation

◆ checkParameters()

void denoptim.programs.mol2graph.Mol2GraphParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 262 of file Mol2GraphParameters.java.

References denoptim.files.FileUtils.checkExists(), denoptim.programs.RunTimeParameters.checkOtherParameters(), denoptim.programs.mol2graph.Mol2GraphParameters.inFile, denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFile, and denoptim.programs.RunTimeParameters.workDir.

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ ensureFragmenterParams()

void denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragmenterParams ( )

private

Definition at line 146 of file Mol2GraphParameters.java.

References denoptim.programs.RunTimeParameters.containsParameters(), denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, and denoptim.programs.RunTimeParameters.setParameters().

Referenced by denoptim.programs.mol2graph.Mol2GraphParameters.getCuttingRules(), denoptim.programs.mol2graph.Mol2GraphParameters.getLinearAngleLimit(), denoptim.programs.mol2graph.Mol2GraphParameters.getScaffoldingPolicy(), and denoptim.programs.mol2graph.Mol2GraphParameters.processParameters().

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◆ ensureFragSpareParams()

void denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragSpareParams ( )

private

Definition at line 156 of file Mol2GraphParameters.java.

References denoptim.programs.RunTimeParameters.containsParameters(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, and denoptim.programs.RunTimeParameters.setParameters().

Referenced by denoptim.programs.mol2graph.Mol2GraphParameters.getFragmentSpace(), and denoptim.programs.mol2graph.Mol2GraphParameters.processParameters().

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◆ getCuttingRules()

List< CuttingRule > denoptim.programs.mol2graph.Mol2GraphParameters.getCuttingRules ( )

Definition at line 106 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragmenterParams(), denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.fragmenter.FragmenterParameters.getCuttingRules(), and denoptim.programs.RunTimeParameters.getParameters().

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getFragmentSpace()

FragmentSpace denoptim.programs.mol2graph.Mol2GraphParameters.getFragmentSpace ( )

Definition at line 136 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragSpareParams(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), and denoptim.programs.RunTimeParameters.getParameters().

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getInputMol()

IAtomContainer denoptim.programs.mol2graph.Mol2GraphParameters.getInputMol ( int i )

Definition at line 85 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.inMols.

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getInputMolsCount()

int denoptim.programs.mol2graph.Mol2GraphParameters.getInputMolsCount ( )

Definition at line 78 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.inMols.

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getLinearAngleLimit()

double denoptim.programs.mol2graph.Mol2GraphParameters.getLinearAngleLimit ( )

Definition at line 126 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragmenterParams(), denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.fragmenter.FragmenterParameters.getLinearAngleLimit(), and denoptim.programs.RunTimeParameters.getParameters().

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getOutFile()

String denoptim.programs.mol2graph.Mol2GraphParameters.getOutFile ( )

Definition at line 92 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFile.

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getOutFormat()

FileFormat denoptim.programs.mol2graph.Mol2GraphParameters.getOutFormat ( )

Definition at line 99 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFormat.

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ getPrintedList()

String denoptim.programs.mol2graph.Mol2GraphParameters.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 230 of file Mol2GraphParameters.java.

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

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◆ getScaffoldingPolicy()

ScaffoldingPolicy denoptim.programs.mol2graph.Mol2GraphParameters.getScaffoldingPolicy ( )

Definition at line 116 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragmenterParams(), denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.RunTimeParameters.getParameters(), and denoptim.programs.fragmenter.FragmenterParameters.getScaffoldingPolicy().

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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◆ interpretKeyword()

void denoptim.programs.mol2graph.Mol2GraphParameters.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 173 of file Mol2GraphParameters.java.

References denoptim.files.FileFormat.GRAPHJSON, denoptim.files.FileFormat.GRAPHSDF, denoptim.programs.mol2graph.Mol2GraphParameters.inFile, denoptim.programs.RunTimeParameters.logFile, denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFile, denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFormat, denoptim.programs.RunTimeParameters.verbosity, and denoptim.programs.RunTimeParameters.workDir.

◆ processParameters()

void denoptim.programs.mol2graph.Mol2GraphParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 299 of file Mol2GraphParameters.java.

References denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragmenterParams(), denoptim.programs.mol2graph.Mol2GraphParameters.ensureFragSpareParams(), denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.fragmenter.FragmenterParameters.getCuttingRules(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.mol2graph.Mol2GraphParameters.inFile, denoptim.programs.mol2graph.Mol2GraphParameters.inMols, denoptim.programs.RunTimeParameters.processOtherParameters(), denoptim.io.DenoptimIO.readAllAtomContainers(), denoptim.io.DenoptimIO.readCuttingRules(), and denoptim.programs.fragmenter.FragmenterParameters.setCuttingRules().

Referenced by denoptim.programs.mol2graph.Mol2Graph.runProgram().

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Member Data Documentation

◆ inFile

String denoptim.programs.mol2graph.Mol2GraphParameters.inFile

private

File with input graphs.

Definition at line 53 of file Mol2GraphParameters.java.

Referenced by denoptim.programs.mol2graph.Mol2GraphParameters.checkParameters(), denoptim.programs.mol2graph.Mol2GraphParameters.interpretKeyword(), and denoptim.programs.mol2graph.Mol2GraphParameters.processParameters().

◆ inMols

List<IAtomContainer> denoptim.programs.mol2graph.Mol2GraphParameters.inMols

private

Input molecular objects.

Definition at line 58 of file Mol2GraphParameters.java.

Referenced by denoptim.programs.mol2graph.Mol2GraphParameters.getInputMol(), denoptim.programs.mol2graph.Mol2GraphParameters.getInputMolsCount(), and denoptim.programs.mol2graph.Mol2GraphParameters.processParameters().

◆ outGraphsFile

String denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFile = null

private

File with output graphs.

Definition at line 63 of file Mol2GraphParameters.java.

Referenced by denoptim.programs.mol2graph.Mol2GraphParameters.checkParameters(), denoptim.programs.mol2graph.Mol2GraphParameters.getOutFile(), and denoptim.programs.mol2graph.Mol2GraphParameters.interpretKeyword().

◆ outGraphsFormat

FileFormat denoptim.programs.mol2graph.Mol2GraphParameters.outGraphsFormat = FileFormat.GRAPHSDF

private

Definition at line 64 of file Mol2GraphParameters.java.

Referenced by denoptim.programs.mol2graph.Mol2GraphParameters.getOutFormat(), and denoptim.programs.mol2graph.Mol2GraphParameters.interpretKeyword().

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

/github/workspace/src/main/java/denoptim/programs/mol2graph/Mol2GraphParameters.java

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Mol2GraphParameters()

Member Function Documentation

◆ checkParameters()

◆ ensureFragmenterParams()

◆ ensureFragSpareParams()

◆ getCuttingRules()

◆ getFragmentSpace()

◆ getInputMol()

◆ getInputMolsCount()

◆ getLinearAngleLimit()

◆ getOutFile()

◆ getOutFormat()

◆ getPrintedList()

◆ getScaffoldingPolicy()

◆ interpretKeyword()

◆ processParameters()

Member Data Documentation

◆ inFile

◆ inMols

◆ outGraphsFile

◆ outGraphsFormat