Parameters and setting related to handling ring closures. More...

Inheritance diagram for denoptim.graph.rings.RingClosureParameters:

Collaboration diagram for denoptim.graph.rings.RingClosureParameters:

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

int	getClosabilityEvalMode ()

int	getMaxNumberRotatableBonds ()

int	getMaxRingSize ()

List< Integer >	getRingSizeBias ()

void	setRingSizeBias (List< Integer > biases)
	Sets the preference for certain ring sizes or the prohibition to generate certain rings (i.e., weight = 0). More...

int	getMinRcaPerType (String type)

int	getMaxRcaPerType (String type)

int	getMinRingClosures ()

int	getMaxRingClosures ()

Map< String, String >	getConstitutionalClosabilityConds ()

void	setConstitutionalClosabilityConds (Map< String, String > ringClosabCondAsSMARTS)
	Sets the list of constitutions that can be formed by ring closure. More...

int	getVerbosity ()
	Returns the level of verbosity, i.e., the amount of log that we want to print. More...

void	allowRingClosures (boolean value)

boolean	allowRingClosures ()

boolean	buildChelatesMode ()

boolean	selectFragmentsFromClosableChains ()

double	getRCDistTolerance ()

double	getConfPathExtraTolerance ()

double	getRCDotPrTolerance ()

double	getLinearityLimit ()

double	getPathConfSearchStep ()

Set< String >	getRequiredRingElements ()

List< BridgeHeadFindingRule >	getBridgeHeadFindingRules ()

String	getRCCLibraryIndexFile ()

String	getRCCLibraryFolder ()

RingClosuresArchive	getRingClosuresArchive ()

boolean	doExhaustiveConfSrch ()

boolean	serializeRCCs ()

boolean	checkInterdependentChains ()

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
	Processes all parameters and initialize related objects. More...

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

Public Attributes
boolean	requireCompleteRingclosure = true
	Flag requesting complete ring closure of all pairs of RCAs in at least one combination of RCAs to consider the calculation successful. More...

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

Protected Attributes
boolean	closeRings = false
	Flag activating the ring closing machinery. More...

boolean	buildChelatesMode = false
	Flag activating procedures favoring formation of chelates. More...

Set< APClass >	metalCoordinatingAPClasses
	List of metal-coordinating APClasses. More...

boolean	selectFragsFromCC = false
	Flag activating the biased selection of closable fragment chains. More...

int	rceMode = -1
	The ring closability evaluation mode: -1= only ring rize bias 0 = only constitution of candidate ring, 1 = only closability of 3D chain, 2 = both 0 and 1. More...

int	maxRotBonds = 7
	Maximum number of rotatable bonds for which conformational space is explored. More...

int	maxRingSize = 9
	Maximum size (number of atoms) in ring closing chain. More...

Map< String, Integer >	minRcaPerType = new HashMap<String,Integer>()
	Minimum number of `RingClosingAttractor`s in a valid graph. More...

Map< String, Integer >	maxRcaPerType = new HashMap<String,Integer>()
	Maximum number of `RingClosingAttractor`s in a valid graph. More...

int	minRingClosures = 0
	Minimum number of `RingClosure`s in a valid graph. More...

int	maxRingClosures = 50
	Maximum number of `RingClosure`s in a valid graph. More...

double	linearityLimit = 178.5
	Maximum value for non-flat bond angle (in degree). More...

double	rcTolDist = 0.33
	Tolerance factor for interatomic distances. More...

double	pathConfSearchExtraTol = 1.1
	Extra tolerance factor for interatomic distances. More...

double	rcMaxDot = -0.75
	Maximum value of dot product between the normalized attachment point vectors at the head and tail of a candidate chain. More...

double	pathConfSearchStep = 12.0
	Torsion angle step for conformational scan of candidate closable chain. More...

List< Integer >	ringSizeBias
	Relative weight of ring sizes to bias the selection of a ring combination among the various alternatives. More...

Map< String, String >	ringClosabCondAsSMARTS
	SMARTS defining the constitution-based ring closability condition. More...

Set< String >	reqElInRings = new HashSet<String>()
	Required elements in closable chains. More...

String	rccIndex = ""
	Pathname of the text file containing the list of visited `RingClosingConformation`s (i.e., index file). More...

String	rccFolder = ""
	Pathname of the root folder containing the archive of serialized `RingClosingConformation`s. More...

boolean	exhaustiveConfSrch = false
	Flag controlling conformational search. More...

boolean	checkInterdepPaths = false
	Flag controlling the ring-closing criterion evaluating the simultaneous closability of interdependent chains. More...

boolean	serializeRCCs = false
	Flag controlling the serialization of the `RingClosingConformations`. More...

List< BridgeHeadFindingRule >	bridgeHeadFindingRules
	Rules that identify the atoms that can become bridge heads to form fused rings. 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 Attributes
RingClosuresArchive	rcArchive
	Collection of information about ring-closability of graph substructures. More...

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...

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 and setting related to handling ring closures.

Author: Marco Foscato

Definition at line 49 of file RingClosureParameters.java.

Constructor & Destructor Documentation

◆ RingClosureParameters()

denoptim.graph.rings.RingClosureParameters.RingClosureParameters ( )

Constructor.

Parameters

paramType the type of parameters this instance is meant to collect.

Definition at line 256 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.bridgeHeadFindingRules, denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.graph.rings.RingClosureParameters.rcArchive, and denoptim.io.DenoptimIO.readBridgeHesFindingRules().

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Member Function Documentation

◆ allowRingClosures() [1/2]

boolean denoptim.graph.rings.RingClosureParameters.allowRingClosures ( )

Definition at line 405 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.closeRings.

◆ allowRingClosures() [2/2]

void denoptim.graph.rings.RingClosureParameters.allowRingClosures ( boolean value )

Definition at line 398 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.closeRings.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), denoptim.graph.DGraph.checkConsistency(), denoptim.ga.GraphOperations.extendGraph(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), denoptim.programs.denovo.GAParameters.processParameters(), and denoptim.ga.EAUtils.setupRings().

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◆ buildChelatesMode()

boolean denoptim.graph.rings.RingClosureParameters.buildChelatesMode ( )

Definition at line 412 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.buildChelatesMode.

◆ checkInterdependentChains()

boolean denoptim.graph.rings.RingClosureParameters.checkInterdependentChains ( )

Definition at line 510 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.checkInterdepPaths.

Referenced by denoptim.graph.rings.CyclicGraphHandler.combineCompatPathSubGraphs(), denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability(), and denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings().

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◆ checkParameters()

void denoptim.graph.rings.RingClosureParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 800 of file RingClosureParameters.java.

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◆ doExhaustiveConfSrch()

boolean denoptim.graph.rings.RingClosureParameters.doExhaustiveConfSrch ( )

Definition at line 496 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.exhaustiveConfSrch.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability(), and denoptim.graph.rings.RingClosureFinder.evaluateClosability().

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◆ getBridgeHeadFindingRules()

List< BridgeHeadFindingRule > denoptim.graph.rings.RingClosureParameters.getBridgeHeadFindingRules ( )

Definition at line 468 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.bridgeHeadFindingRules.

◆ getClosabilityEvalMode()

int denoptim.graph.rings.RingClosureParameters.getClosabilityEvalMode ( )

Definition at line 276 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.rceMode.

Referenced by denoptim.graph.rings.PathClosabilityTools.isCloseable().

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◆ getConfPathExtraTolerance()

double denoptim.graph.rings.RingClosureParameters.getConfPathExtraTolerance ( )

Definition at line 433 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.pathConfSearchExtraTol.

Referenced by denoptim.graph.rings.RingClosureFinder.evaluateClosability().

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◆ getConstitutionalClosabilityConds()

Map< String, String > denoptim.graph.rings.RingClosureParameters.getConstitutionalClosabilityConds ( )

Definition at line 365 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.ringClosabCondAsSMARTS.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability().

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◆ getLinearityLimit()

double denoptim.graph.rings.RingClosureParameters.getLinearityLimit ( )

Definition at line 447 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.linearityLimit.

Referenced by denoptim.graph.rings.RingClosureFinder.evaluateClosability().

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◆ getMaxNumberRotatableBonds()

int denoptim.graph.rings.RingClosureParameters.getMaxNumberRotatableBonds ( )

Definition at line 283 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.maxRotBonds.

Referenced by denoptim.graph.rings.RingClosureFinder.evaluateClosability().

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◆ getMaxRcaPerType()

int denoptim.graph.rings.RingClosureParameters.getMaxRcaPerType ( String type )

Parameters

type	the elemental symbol of the RCA to consider.

Returns: the maximum allowed number of RCAs or 0, if not set.

Definition at line 341 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.maxRcaPerType.

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

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◆ getMaxRingClosures()

int denoptim.graph.rings.RingClosureParameters.getMaxRingClosures ( )

Definition at line 358 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.maxRingClosures.

Referenced by denoptim.ga.EAUtils.setupRings().

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◆ getMaxRingSize()

int denoptim.graph.rings.RingClosureParameters.getMaxRingSize ( )

Definition at line 290 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.maxRingSize.

Referenced by denoptim.ga.GraphOperations.addFusedRing(), denoptim.graph.rings.RingSizeManager.calculateCompatibilityOfAllRCAPairs(), denoptim.graph.rings.RingSizeManager.getRSBiasedListOfCandidates(), and denoptim.ga.GraphOperationsTest.testAddRing().

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◆ getMinRcaPerType()

int denoptim.graph.rings.RingClosureParameters.getMinRcaPerType ( String type )

Parameters

type	the elemental symbol of the RCA to consider.

Returns: the minimum allowed number of RCAs or 0, if not set.

Definition at line 327 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.minRcaPerType.

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

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◆ getMinRingClosures()

int denoptim.graph.rings.RingClosureParameters.getMinRingClosures ( )

Definition at line 351 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.minRingClosures.

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

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◆ getPathConfSearchStep()

double denoptim.graph.rings.RingClosureParameters.getPathConfSearchStep ( )

Definition at line 454 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.pathConfSearchStep.

Referenced by denoptim.graph.rings.CyclicGraphHandler.ClosableConf.canCoexistWith(), and denoptim.graph.rings.RingClosureFinder.evaluateClosability().

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◆ getPrintedList()

String denoptim.graph.rings.RingClosureParameters.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 907 of file RingClosureParameters.java.

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

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◆ getRCCLibraryFolder()

String denoptim.graph.rings.RingClosureParameters.getRCCLibraryFolder ( )

Definition at line 482 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.rccFolder.

Referenced by denoptim.graph.rings.RingClosuresArchive.getRCCsFromArchive(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

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◆ getRCCLibraryIndexFile()

String denoptim.graph.rings.RingClosureParameters.getRCCLibraryIndexFile ( )

Definition at line 475 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.rccIndex.

Referenced by denoptim.graph.rings.RingClosuresArchive.RingClosuresArchive(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

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◆ getRCDistTolerance()

double denoptim.graph.rings.RingClosureParameters.getRCDistTolerance ( )

Definition at line 426 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.rcTolDist.

Referenced by denoptim.molecularmodeling.RingClosureTool.closeRings(), and denoptim.graph.rings.RingClosure.getClosabilityConditions().

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◆ getRCDotPrTolerance()

double denoptim.graph.rings.RingClosureParameters.getRCDotPrTolerance ( )

Definition at line 440 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.rcMaxDot.

Referenced by denoptim.molecularmodeling.RingClosureTool.closeRings(), and denoptim.graph.rings.RingClosure.getClosabilityConditions().

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◆ getRequiredRingElements()

Set< String > denoptim.graph.rings.RingClosureParameters.getRequiredRingElements ( )

Definition at line 461 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.reqElInRings.

Referenced by denoptim.graph.rings.PathClosabilityTools.evaluateConstitutionalClosability().

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◆ getRingClosuresArchive()

RingClosuresArchive denoptim.graph.rings.RingClosureParameters.getRingClosuresArchive ( )

Definition at line 489 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.rcArchive.

Referenced by denoptim.ga.EAUtils.buildGraph(), and denoptim.graph.rings.PathClosabilityTools.evaluate3DPathClosability().

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◆ getRingSizeBias()

List< Integer > denoptim.graph.rings.RingClosureParameters.getRingSizeBias ( )

Returns: the list of biases for ring size. Each value is the weight of the preference for rings of the size equal to the index of the value in the list.

Definition at line 302 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.ringSizeBias.

Referenced by denoptim.ga.GraphOperations.addFusedRing(), denoptim.gui.FSParametersForm.FSParametersForm(), and denoptim.graph.rings.RingSizeManager.RingSizeManager().

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◆ getVerbosity()

int denoptim.graph.rings.RingClosureParameters.getVerbosity ( )

Returns the level of verbosity, i.e., the amount of log that we want to print.

Returns: the level of verbosity.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 391 of file RingClosureParameters.java.

References denoptim.programs.RunTimeParameters.verbosity.

Referenced by denoptim.graph.rings.RingClosuresArchive.getRCCsOfChain().

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◆ interpretKeyword()

void denoptim.graph.rings.RingClosureParameters.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 517 of file RingClosureParameters.java.

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◆ processParameters()

void denoptim.graph.rings.RingClosureParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 893 of file RingClosureParameters.java.

References denoptim.programs.RunTimeParameters.processOtherParameters(), and denoptim.graph.rings.RingClosureParameters.rcArchive.

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◆ selectFragmentsFromClosableChains()

boolean denoptim.graph.rings.RingClosureParameters.selectFragmentsFromClosableChains ( )

Definition at line 419 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.selectFragsFromCC.

Referenced by denoptim.ga.GraphOperations.extendGraph().

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◆ serializeRCCs()

boolean denoptim.graph.rings.RingClosureParameters.serializeRCCs ( )

Definition at line 503 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.serializeRCCs.

◆ setConstitutionalClosabilityConds()

void denoptim.graph.rings.RingClosureParameters.setConstitutionalClosabilityConds ( Map< String, String > ringClosabCondAsSMARTS )

Sets the list of constitutions that can be formed by ring closure.

SMARTS are used to define such constitutions. Note that the ring-closing attractors are not considered in the definition of the constitution of the ring.

Parameters

ringClosabCondAsSMARTS a map where each entry is a rule that defined constitutions that can be formed. In each entry, the key is the name of the rule and is used only for logging, and the value is the SMARTS query that must be matched for a candidate ring to be accepted.

Definition at line 383 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.ringClosabCondAsSMARTS.

Referenced by denoptim.graph.rings.PathClosabilityToolsTest.testEvaluateConstitutionalClosability().

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◆ setRingSizeBias()

void denoptim.graph.rings.RingClosureParameters.setRingSizeBias ( List< Integer > biases )

Sets the preference for certain ring sizes or the prohibition to generate certain rings (i.e., weight = 0).

Parameters

biases the list of biases for ring size. Each value is the weight
of the preference for rings of the size equal to the index of the value in the list.

Definition at line 316 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.ringSizeBias.

Referenced by denoptim.ga.GraphOperationsTest.testAddFusedRings(), denoptim.ga.GraphOperationsTest.testAddRing(), denoptim.graph.rings.RandomCombOfRingIteratorTest.testEvaluateConstitutionalClosability(), and denoptim.graph.rings.RingSizeManagerTest.testEvaluateRCVPair().

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Member Data Documentation

◆ bridgeHeadFindingRules

List<BridgeHeadFindingRule> denoptim.graph.rings.RingClosureParameters.bridgeHeadFindingRules

protected

Rules that identify the atoms that can become bridge heads to form fused rings.

Definition at line 248 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getBridgeHeadFindingRules(), denoptim.graph.rings.RingClosureParameters.interpretKeyword(), and denoptim.graph.rings.RingClosureParameters.RingClosureParameters().

◆ buildChelatesMode

boolean denoptim.graph.rings.RingClosureParameters.buildChelatesMode = false

protected

Flag activating procedures favoring formation of chelates.

Definition at line 66 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.buildChelatesMode(), denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.interpretKeyword(), denoptim.graph.DGraph.makeAllGraphsWithDifferentRingSets(), and denoptim.ga.EAUtils.setupRings().

◆ checkInterdepPaths

boolean denoptim.graph.rings.RingClosureParameters.checkInterdepPaths = false

protected

Flag controlling the ring-closing criterion evaluating the simultaneous closability of interdependent chains.

If true requires the evaluation of interdependent chains.

Definition at line 235 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkInterdependentChains(), denoptim.graph.rings.RingClosureParameters.checkParameters(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ closeRings

boolean denoptim.graph.rings.RingClosureParameters.closeRings = false

protected

Flag activating the ring closing machinery.

Definition at line 54 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.allowRingClosures(), denoptim.graph.rings.RingClosureParameters.checkParameters(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ exhaustiveConfSrch

boolean denoptim.graph.rings.RingClosureParameters.exhaustiveConfSrch = false

protected

Flag controlling conformational search.

If true the whole torsional space is scanned looking for ring closing conformations. WARNING! This is very time consuming, but is needed for the current implementation of the iterdependent ring criterion.

Definition at line 228 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.doExhaustiveConfSrch(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ linearityLimit

double denoptim.graph.rings.RingClosureParameters.linearityLimit = 178.5

protected

Maximum value for non-flat bond angle (in degree).

Definition at line 127 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getLinearityLimit(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ maxRcaPerType

Map<String,Integer> denoptim.graph.rings.RingClosureParameters.maxRcaPerType = new HashMap<String,Integer>()

protected

Maximum number of RingClosingAttractors in a valid graph.

Definition at line 112 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.getMaxRcaPerType(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ maxRingClosures

int denoptim.graph.rings.RingClosureParameters.maxRingClosures = 50

protected

Maximum number of RingClosures in a valid graph.

Definition at line 122 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.getMaxRingClosures(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ maxRingSize

int denoptim.graph.rings.RingClosureParameters.maxRingSize = 9

protected

Maximum size (number of atoms) in ring closing chain.

The shortest path is considered.

Definition at line 102 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getMaxRingSize(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ maxRotBonds

int denoptim.graph.rings.RingClosureParameters.maxRotBonds = 7

protected

Maximum number of rotatable bonds for which conformational space is explored.

Definition at line 96 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getMaxNumberRotatableBonds(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ metalCoordinatingAPClasses

Set<APClass> denoptim.graph.rings.RingClosureParameters.metalCoordinatingAPClasses

protected

Initial value:

=

new HashSet<APClass>()

List of metal-coordinating APClasses.

Used to identify 'orphan' metal-coordinating sites that give rise to coordination isomerism (i.e., we have build a specific isomer, but the existence of unused metal- coordinating groups opens for the possibility of binding the metal/s with a different combination of groups).

Definition at line 75 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ minRcaPerType

Map<String,Integer> denoptim.graph.rings.RingClosureParameters.minRcaPerType = new HashMap<String,Integer>()

protected

Minimum number of RingClosingAttractors in a valid graph.

Definition at line 107 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.getMinRcaPerType(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ minRingClosures

int denoptim.graph.rings.RingClosureParameters.minRingClosures = 0

protected

Minimum number of RingClosures in a valid graph.

Definition at line 117 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.getMinRingClosures(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ pathConfSearchExtraTol

double denoptim.graph.rings.RingClosureParameters.pathConfSearchExtraTol = 1.1

protected

Extra tolerance factor for interatomic distances.

This value (ep) is multiplied to the tolerance factor (p) when discrete as opposite to continue variation of torsion angles is performed. With the normal tolerance factor (p) and the lengths of the AP vectors l_H and l_T, the accepted deviation to an interatomic distance (dt) is calculated as dt = ep * p * (l_H + l_T) / 2

Definition at line 152 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getConfPathExtraTolerance(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ pathConfSearchStep

double denoptim.graph.rings.RingClosureParameters.pathConfSearchStep = 12.0

protected

Torsion angle step for conformational scan of candidate closable chain.

Definition at line 164 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getPathConfSearchStep(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ rcArchive

RingClosuresArchive denoptim.graph.rings.RingClosureParameters.rcArchive

private

Collection of information about ring-closability of graph substructures.

Definition at line 220 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getRingClosuresArchive(), denoptim.graph.rings.RingClosureParameters.processParameters(), and denoptim.graph.rings.RingClosureParameters.RingClosureParameters().

◆ rccFolder

String denoptim.graph.rings.RingClosureParameters.rccFolder = ""

protected

Pathname of the root folder containing the archive of serialized RingClosingConformations.

Definition at line 215 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.getRCCLibraryFolder(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ rccIndex

String denoptim.graph.rings.RingClosureParameters.rccIndex = ""

protected

Pathname of the text file containing the list of visited RingClosingConformations (i.e., index file).

The index file is machine-written and is bound to the corresponding libraries of fragments.

Definition at line 209 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getRCCLibraryIndexFile(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ rceMode

int denoptim.graph.rings.RingClosureParameters.rceMode = -1

protected

The ring closability evaluation mode: -1= only ring rize bias 0 = only constitution of candidate ring, 1 = only closability of 3D chain, 2 = both 0 and 1.

Definition at line 90 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.getClosabilityEvalMode(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ rcMaxDot

double denoptim.graph.rings.RingClosureParameters.rcMaxDot = -0.75

protected

Maximum value of dot product between the normalized attachment point vectors at the head and tail of a candidate chain.

Note that perfect alignment implies a dot product of -1.0.

Definition at line 159 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getRCDotPrTolerance(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ rcTolDist

double denoptim.graph.rings.RingClosureParameters.rcTolDist = 0.33

protected

Tolerance factor for interatomic distances.

This value is the percentage (p) of the average between the attachment point vector lengths at the head (l_H) and tail (l_T) of a candidate chain. dt = p * (l_H + l_T) / 2 Interatomic distance criteria are satisfied with a deviation of +/- dt

Definition at line 139 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getRCDistTolerance(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ reqElInRings

Set<String> denoptim.graph.rings.RingClosureParameters.reqElInRings = new HashSet<String>()

protected

Required elements in closable chains.

Definition at line 201 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getRequiredRingElements(), and denoptim.graph.rings.RingClosureParameters.interpretKeyword().

◆ requireCompleteRingclosure

boolean denoptim.graph.rings.RingClosureParameters.requireCompleteRingclosure = true

Flag requesting complete ring closure of all pairs of RCAs in at least one combination of RCAs to consider the calculation successful.

Definition at line 61 of file RingClosureParameters.java.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure().

◆ ringClosabCondAsSMARTS

Map<String,String> denoptim.graph.rings.RingClosureParameters.ringClosabCondAsSMARTS

protected

Initial value:

=

new HashMap<String,String>()

SMARTS defining the constitution-based ring closability condition.

Definition at line 195 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getConstitutionalClosabilityConds(), denoptim.graph.rings.RingClosureParameters.interpretKeyword(), and denoptim.graph.rings.RingClosureParameters.setConstitutionalClosabilityConds().

◆ ringSizeBias

List<Integer> denoptim.graph.rings.RingClosureParameters.ringSizeBias

protected

Initial value:

= new ArrayList<Integer>()
        {
            
            private static final long serialVersionUID = 1L;
            {
                for (int i=0; i<maxRingSize+1; i++)
                {
                    add(0);
                }
                if (maxRingSize>=7)
                {
                        
                        
                        set(5,2);
                        set(6,4);
                        set(7,1);
                }
            }
        }

Relative weight of ring sizes to bias the selection of a ring combination among the various alternatives.

Definition at line 170 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.getRingSizeBias(), denoptim.graph.rings.RingClosureParameters.interpretKeyword(), and denoptim.graph.rings.RingClosureParameters.setRingSizeBias().

◆ selectFragsFromCC

boolean denoptim.graph.rings.RingClosureParameters.selectFragsFromCC = false

protected

Flag activating the biased selection of closable fragment chains.

Definition at line 81 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.checkParameters(), denoptim.graph.rings.RingClosureParameters.interpretKeyword(), and denoptim.graph.rings.RingClosureParameters.selectFragmentsFromClosableChains().

◆ serializeRCCs

boolean denoptim.graph.rings.RingClosureParameters.serializeRCCs = false

protected

Flag controlling the serialization of the RingClosingConformations.

This flag is activated by the keyword providing the pathname of the root folder of the RCCs archive

Definition at line 242 of file RingClosureParameters.java.

Referenced by denoptim.graph.rings.RingClosureParameters.interpretKeyword(), denoptim.graph.rings.RingClosureParameters.serializeRCCs(), and denoptim.graph.rings.RingClosuresArchive.storeEntry().

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

/github/workspace/src/main/java/denoptim/graph/rings/RingClosureParameters.java

Public Member Functions

Public Attributes

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RingClosureParameters()

Member Function Documentation

◆ allowRingClosures() [1/2]

◆ allowRingClosures() [2/2]

◆ buildChelatesMode()

◆ checkInterdependentChains()

◆ checkParameters()

◆ doExhaustiveConfSrch()

◆ getBridgeHeadFindingRules()

◆ getClosabilityEvalMode()

◆ getConfPathExtraTolerance()

◆ getConstitutionalClosabilityConds()

◆ getLinearityLimit()

◆ getMaxNumberRotatableBonds()

◆ getMaxRcaPerType()

◆ getMaxRingClosures()

◆ getMaxRingSize()

◆ getMinRcaPerType()

◆ getMinRingClosures()

◆ getPathConfSearchStep()

◆ getPrintedList()

◆ getRCCLibraryFolder()

◆ getRCCLibraryIndexFile()

◆ getRCDistTolerance()

◆ getRCDotPrTolerance()

◆ getRequiredRingElements()

◆ getRingClosuresArchive()

◆ getRingSizeBias()

◆ getVerbosity()

◆ interpretKeyword()

◆ processParameters()

◆ selectFragmentsFromClosableChains()

◆ serializeRCCs()

◆ setConstitutionalClosabilityConds()

◆ setRingSizeBias()

Member Data Documentation

◆ bridgeHeadFindingRules

◆ buildChelatesMode

◆ checkInterdepPaths

◆ closeRings

◆ exhaustiveConfSrch

◆ linearityLimit

◆ maxRcaPerType

◆ maxRingClosures

◆ maxRingSize

◆ maxRotBonds

◆ metalCoordinatingAPClasses

◆ minRcaPerType

◆ minRingClosures

◆ pathConfSearchExtraTol

◆ pathConfSearchStep

◆ rcArchive

◆ rccFolder

◆ rccIndex

◆ rceMode

◆ rcMaxDot

◆ rcTolDist

◆ reqElInRings

◆ requireCompleteRingclosure

◆ ringClosabCondAsSMARTS

◆ ringSizeBias

◆ selectFragsFromCC

◆ serializeRCCs