Parameters defining the fragment space. More...

Inheritance diagram for denoptim.fragspace.FragmentSpaceParameters:

Collaboration diagram for denoptim.fragspace.FragmentSpaceParameters:

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

	FragmentSpaceParameters (FragmentSpace fs)
	Constructor of a default set of parameters coupled with a given fragment space. More...

int	getMaxHeavyAtom ()

int	getMaxRotatableBond ()

double	getMaxMW ()

boolean	enforceSymmetry ()

boolean	symmetryConstraints ()

String	getRotSpaceDefFile ()

String	getPathnameToAppendedFragments ()

String	getPathnameToAppendedScaffolds ()

FragmentSpace	getFragmentSpace ()

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

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

void	processParameters () throws DENOPTIMException
	Read the information collected in the parameters stored in this class and create the fragment space accordingly. More...

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

void	setFragmentSpace (FragmentSpace fragmentSpace)
	Sets the fragment space linked to these parameters. 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...

Protected Attributes
String	scaffoldLibFile = ""
	Pathname of the file containing the molecular representation of building blocks: scaffolds section - fragments that can be used as seed to grow a new molecule. More...

String	fragmentLibFile = ""
	PathName of the file containing the molecular representation of building blocks: fragment section - fragments for general use. More...

String	cappingLibFile = ""
	Pathname of the file containing the molecular representation of building blocks: capping group section - fragments with only one attachment point used to saturate unused attachment points on a graph. More...

String	compMatrixFile = ""
	Pathname of the file containing the compatibility matrix, bond order to AP-class relation, and forbidden ends list. More...

String	rcCompMatrixFile = ""
	Pathname of the file containing the RC-compatibility matrix. More...

String	rotBndsFile = ""
	Rotatable bonds definition file. More...

int	maxHeavyAtom = 100
	Maximum number of heavy (non-hydrogen) atoms accepted. More...

int	maxRotatableBond = 20
	Maximum number of rotatable bonds accepted. More...

double	maxMW = 500
	Maximum molecular weight accepted. More...

boolean	enforceSymmetry = false
	Flag enforcing constitutional symmetry. More...

boolean	symmetryConstraints = false
	Flag for application of selected constitutional symmetry constraints. 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...

Private Member Functions
	FragmentSpaceParameters (ParametersType paramType)
	Constructor. More...

Private Attributes
HashMap< APClass, Double >	symmConstraintsMap
	List of constitutional symmetry constraints. More...

FragmentSpace	buildingBlocksSpace = null

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...

Detailed Description

Parameters defining the fragment space.

Author: Marco Foscato

Definition at line 38 of file FragmentSpaceParameters.java.

Constructor & Destructor Documentation

◆ FragmentSpaceParameters() [1/3]

denoptim.fragspace.FragmentSpaceParameters.FragmentSpaceParameters ( ParametersType paramType )

private

Constructor.

Definition at line 115 of file FragmentSpaceParameters.java.

References denoptim.programs.RunTimeParameters.paramType.

◆ FragmentSpaceParameters() [2/3]

denoptim.fragspace.FragmentSpaceParameters.FragmentSpaceParameters ( )

Constructor.

Definition at line 125 of file FragmentSpaceParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS.

◆ FragmentSpaceParameters() [3/3]

denoptim.fragspace.FragmentSpaceParameters.FragmentSpaceParameters ( FragmentSpace fs )

Constructor of a default set of parameters coupled with a given fragment space.

Parameters

fs

Definition at line 137 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.buildingBlocksSpace, and denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS.

Member Function Documentation

◆ checkParameters()

void denoptim.fragspace.FragmentSpaceParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 336 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.cappingLibFile, denoptim.files.FileUtils.checkExists(), denoptim.programs.RunTimeParameters.checkOtherParameters(), denoptim.fragspace.FragmentSpaceParameters.compMatrixFile, denoptim.fragspace.FragmentSpaceParameters.fragmentLibFile, denoptim.programs.RunTimeParameters.getLogger(), denoptim.fragspace.FragmentSpaceParameters.rcCompMatrixFile, denoptim.fragspace.FragmentSpaceParameters.rotBndsFile, and denoptim.fragspace.FragmentSpaceParameters.scaffoldLibFile.

Referenced by denoptim.gui.FSParamsDialog.makeFragSpace().

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◆ enforceSymmetry()

boolean denoptim.fragspace.FragmentSpaceParameters.enforceSymmetry ( )

Definition at line 166 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.enforceSymmetry.

◆ getFragmentSpace()

FragmentSpace denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace ( )

Definition at line 203 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.buildingBlocksSpace.

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◆ getMaxHeavyAtom()

int denoptim.fragspace.FragmentSpaceParameters.getMaxHeavyAtom ( )

Definition at line 145 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.maxHeavyAtom.

Referenced by denoptim.graph.DGraph.checkConsistency(), and denoptim.ga.GraphOperations.extendGraph().

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◆ getMaxMW()

double denoptim.fragspace.FragmentSpaceParameters.getMaxMW ( )

Definition at line 159 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.maxMW.

Referenced by denoptim.graph.DGraph.checkConsistency().

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◆ getMaxRotatableBond()

int denoptim.fragspace.FragmentSpaceParameters.getMaxRotatableBond ( )

Definition at line 152 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.maxRotatableBond.

Referenced by denoptim.graph.DGraph.checkConsistency().

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◆ getPathnameToAppendedFragments()

String denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedFragments ( )

Definition at line 187 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.fragmentLibFile.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ getPathnameToAppendedScaffolds()

String denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedScaffolds ( )

Definition at line 195 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.scaffoldLibFile.

Referenced by denoptim.fragspace.FragmentSpace.addFusedRingsToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToFragmentLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingAddedToScaffoldLibrary(), denoptim.fragspace.FragmentSpaceTest.testFusedRingOnlyAddedOnce(), and denoptim.fragspace.FragmentSpaceTest.testUseWholeMolGeometryForExtractedTemplates().

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◆ getPrintedList()

String denoptim.fragspace.FragmentSpaceParameters.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 425 of file FragmentSpaceParameters.java.

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

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◆ getRotSpaceDefFile()

String denoptim.fragspace.FragmentSpaceParameters.getRotSpaceDefFile ( )

Definition at line 180 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.rotBndsFile.

Referenced by denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets().

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◆ interpretKeyword()

void denoptim.fragspace.FragmentSpaceParameters.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 is the parameter cannot be configured from the given value.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 210 of file FragmentSpaceParameters.java.

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◆ processParameters()

void denoptim.fragspace.FragmentSpaceParameters.processParameters ( ) throws DENOPTIMException

Read the information collected in the parameters stored in this class and create the fragment space accordingly.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 408 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.buildingBlocksSpace, denoptim.fragspace.FragmentSpaceParameters.cappingLibFile, denoptim.fragspace.FragmentSpaceParameters.compMatrixFile, denoptim.fragspace.FragmentSpaceParameters.fragmentLibFile, denoptim.programs.RunTimeParameters.processOtherParameters(), denoptim.fragspace.FragmentSpaceParameters.rcCompMatrixFile, denoptim.fragspace.FragmentSpaceParameters.scaffoldLibFile, and denoptim.fragspace.FragmentSpaceParameters.symmConstraintsMap.

Referenced by denoptim.gui.FSParamsDialog.makeFragSpace().

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◆ setFragmentSpace()

void denoptim.fragspace.FragmentSpaceParameters.setFragmentSpace ( FragmentSpace fragmentSpace )

Sets the fragment space linked to these parameters.

This method should be used only in unit test to by-pass the creation of a FragmentSpace from parameters.

Parameters

fragmentSpace

Definition at line 458 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.buildingBlocksSpace.

Referenced by denoptim.fragspace.FragmentSpace.define().

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◆ symmetryConstraints()

boolean denoptim.fragspace.FragmentSpaceParameters.symmetryConstraints ( )

Definition at line 173 of file FragmentSpaceParameters.java.

References denoptim.fragspace.FragmentSpaceParameters.symmetryConstraints.

Member Data Documentation

◆ buildingBlocksSpace

FragmentSpace denoptim.fragspace.FragmentSpaceParameters.buildingBlocksSpace = null

private

Definition at line 108 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.FragmentSpaceParameters(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.fragspace.FragmentSpaceParameters.processParameters(), and denoptim.fragspace.FragmentSpaceParameters.setFragmentSpace().

◆ cappingLibFile

String denoptim.fragspace.FragmentSpaceParameters.cappingLibFile = ""

protected

Pathname of the file containing the molecular representation of building blocks: capping group section - fragments with only one attachment point used to saturate unused attachment points on a graph.

Definition at line 59 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.checkParameters(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragmentSpaceParameters.processParameters().

◆ compMatrixFile

String denoptim.fragspace.FragmentSpaceParameters.compMatrixFile = ""

protected

Pathname of the file containing the compatibility matrix, bond order to AP-class relation, and forbidden ends list.

Definition at line 65 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.checkParameters(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragmentSpaceParameters.processParameters().

◆ enforceSymmetry

boolean denoptim.fragspace.FragmentSpaceParameters.enforceSymmetry = false

protected

Flag enforcing constitutional symmetry.

Definition at line 95 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.enforceSymmetry(), denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), denoptim.fragspace.FragmentSpace.imposeSymmetryOnAPsOfClass(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragsCombinationIterator.next().

◆ fragmentLibFile

String denoptim.fragspace.FragmentSpaceParameters.fragmentLibFile = ""

protected

PathName of the file containing the molecular representation of building blocks: fragment section - fragments for general use.

Definition at line 51 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.checkParameters(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedFragments(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragmentSpaceParameters.processParameters().

◆ maxHeavyAtom

int denoptim.fragspace.FragmentSpaceParameters.maxHeavyAtom = 100

protected

Maximum number of heavy (non-hydrogen) atoms accepted.

Definition at line 80 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.getMaxHeavyAtom(), and denoptim.fragspace.FragmentSpaceParameters.interpretKeyword().

◆ maxMW

double denoptim.fragspace.FragmentSpaceParameters.maxMW = 500

protected

Maximum molecular weight accepted.

Definition at line 90 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.getMaxMW(), and denoptim.fragspace.FragmentSpaceParameters.interpretKeyword().

◆ maxRotatableBond

int denoptim.fragspace.FragmentSpaceParameters.maxRotatableBond = 20

protected

Maximum number of rotatable bonds accepted.

Definition at line 85 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.getMaxRotatableBond(), and denoptim.fragspace.FragmentSpaceParameters.interpretKeyword().

◆ rcCompMatrixFile

String denoptim.fragspace.FragmentSpaceParameters.rcCompMatrixFile = ""

protected

Pathname of the file containing the RC-compatibility matrix.

Definition at line 70 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.checkParameters(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragmentSpaceParameters.processParameters().

◆ rotBndsFile

String denoptim.fragspace.FragmentSpaceParameters.rotBndsFile = ""

protected

Rotatable bonds definition file.

Definition at line 75 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.checkParameters(), denoptim.fragspace.FragmentSpaceParameters.getRotSpaceDefFile(), and denoptim.fragspace.FragmentSpaceParameters.interpretKeyword().

◆ scaffoldLibFile

String denoptim.fragspace.FragmentSpaceParameters.scaffoldLibFile = ""

protected

Pathname of the file containing the molecular representation of building blocks: scaffolds section - fragments that can be used as seed to grow a new molecule.

Definition at line 45 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.checkParameters(), denoptim.fragspace.FragmentSpaceParameters.getPathnameToAppendedScaffolds(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragmentSpaceParameters.processParameters().

◆ symmConstraintsMap

HashMap<APClass, Double> denoptim.fragspace.FragmentSpaceParameters.symmConstraintsMap

private

Initial value:

=

new HashMap<APClass, Double>()

List of constitutional symmetry constraints.

Definition at line 105 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), and denoptim.fragspace.FragmentSpaceParameters.processParameters().

◆ symmetryConstraints

boolean denoptim.fragspace.FragmentSpaceParameters.symmetryConstraints = false

protected

Flag for application of selected constitutional symmetry constraints.

Definition at line 100 of file FragmentSpaceParameters.java.

Referenced by denoptim.fragspace.FragsCombinationIterator.FragsCombinationIterator(), denoptim.fragspace.FragmentSpaceParameters.interpretKeyword(), denoptim.fragspace.FragsCombinationIterator.next(), and denoptim.fragspace.FragmentSpaceParameters.symmetryConstraints().

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

/github/workspace/src/main/java/denoptim/fragspace/FragmentSpaceParameters.java

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FragmentSpaceParameters() [1/3]

◆ FragmentSpaceParameters() [2/3]

◆ FragmentSpaceParameters() [3/3]

Member Function Documentation

◆ checkParameters()

◆ enforceSymmetry()

◆ getFragmentSpace()

◆ getMaxHeavyAtom()

◆ getMaxMW()

◆ getMaxRotatableBond()

◆ getPathnameToAppendedFragments()

◆ getPathnameToAppendedScaffolds()

◆ getPrintedList()

◆ getRotSpaceDefFile()

◆ interpretKeyword()

◆ processParameters()

◆ setFragmentSpace()

◆ symmetryConstraints()

Member Data Documentation

◆ buildingBlocksSpace

◆ cappingLibFile

◆ compMatrixFile

◆ enforceSymmetry

◆ fragmentLibFile

◆ maxHeavyAtom

◆ maxMW

◆ maxRotatableBond

◆ rcCompMatrixFile

◆ rotBndsFile

◆ scaffoldLibFile

◆ symmConstraintsMap

◆ symmetryConstraints