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DENOPTIM
Public Member Functions | Public Attributes | Protected Attributes | Private Attributes | List of all members
denoptim.graph.rings.RingClosureParameters Class Reference

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

Inheritance diagram for denoptim.graph.rings.RingClosureParameters:
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Collaboration diagram for denoptim.graph.rings.RingClosureParameters:
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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 ()
 
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 RingClosingAttractors in a valid graph. More...
 
Map< String, Integer > maxRcaPerType = new HashMap<String,Integer>()
 Maximum number of RingClosingAttractors in a valid graph. More...
 
int minRingClosures = 0
 Minimum number of RingClosures in a valid graph. More...
 
int maxRingClosures = 50
 Maximum number of RingClosures 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 RingClosingConformations (i.e., index file). More...
 
String rccFolder = ""
 Pathname of the root folder containing the archive of serialized RingClosingConformations. 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...
 
- 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 44 of file RingClosureParameters.java.

Constructor & Destructor Documentation

◆ RingClosureParameters()

denoptim.graph.rings.RingClosureParameters.RingClosureParameters ( )

Constructor.

Parameters
paramTypethe type of parameters this instance is meant to collect.

Definition at line 245 of file RingClosureParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, and denoptim.graph.rings.RingClosureParameters.rcArchive.

Member Function Documentation

◆ allowRingClosures() [1/2]

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

Definition at line 382 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.closeRings.

◆ allowRingClosures() [2/2]

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

Definition at line 375 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 389 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.buildChelatesMode.

◆ checkInterdependentChains()

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

Definition at line 480 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 756 of file RingClosureParameters.java.

References denoptim.logging.StaticLogger.appLogger, denoptim.graph.rings.RingClosureParameters.buildChelatesMode, denoptim.files.FileUtils.checkExists(), denoptim.graph.rings.RingClosureParameters.checkInterdepPaths, denoptim.programs.RunTimeParameters.checkOtherParameters(), denoptim.graph.rings.RingClosureParameters.closeRings, denoptim.graph.rings.RingClosureParameters.exhaustiveConfSrch, denoptim.graph.rings.RingClosureParameters.maxRcaPerType, denoptim.graph.rings.RingClosureParameters.maxRingClosures, denoptim.graph.rings.RingClosureParameters.minRcaPerType, denoptim.graph.rings.RingClosureParameters.minRingClosures, denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.graph.rings.RingClosureParameters.rccFolder, denoptim.graph.rings.RingClosureParameters.rceMode, and denoptim.graph.rings.RingClosureParameters.selectFragsFromCC.

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◆ doExhaustiveConfSrch()

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

Definition at line 466 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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◆ getClosabilityEvalMode()

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

Definition at line 253 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 410 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 342 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 424 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 260 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
typethe elemental symbol of the RCA to consider.
Returns
the maximum allowed number of RCAs or 0, if not set.

Definition at line 318 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 335 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 267 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.maxRingSize.

Referenced by 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
typethe elemental symbol of the RCA to consider.
Returns
the minimum allowed number of RCAs or 0, if not set.

Definition at line 304 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 328 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 431 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 863 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 452 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 445 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 403 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 417 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 438 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 459 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 279 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.ringSizeBias.

Referenced by 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 368 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
keythe keyword as string
valuethe value as a string
Exceptions
DENOPTIMExceptionis the parameter cannot be configured from the given value.

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 487 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.buildChelatesMode, denoptim.graph.rings.RingClosureParameters.checkInterdepPaths, denoptim.graph.rings.RingClosureParameters.closeRings, denoptim.graph.rings.RingClosureParameters.exhaustiveConfSrch, denoptim.graph.rings.RingClosureParameters.linearityLimit, denoptim.graph.APClass.make(), denoptim.graph.rings.RingClosureParameters.maxRcaPerType, denoptim.graph.rings.RingClosureParameters.maxRingClosures, denoptim.graph.rings.RingClosureParameters.maxRingSize, denoptim.graph.rings.RingClosureParameters.maxRotBonds, denoptim.graph.rings.RingClosureParameters.metalCoordinatingAPClasses, denoptim.graph.rings.RingClosureParameters.minRcaPerType, denoptim.graph.rings.RingClosureParameters.minRingClosures, denoptim.graph.rings.RingClosureParameters.pathConfSearchExtraTol, denoptim.graph.rings.RingClosureParameters.pathConfSearchStep, denoptim.graph.rings.RingClosureParameters.rccFolder, denoptim.graph.rings.RingClosureParameters.rccIndex, denoptim.graph.rings.RingClosureParameters.rceMode, denoptim.graph.rings.RingClosureParameters.rcMaxDot, denoptim.graph.rings.RingClosureParameters.rcTolDist, denoptim.graph.rings.RingClosureParameters.reqElInRings, denoptim.graph.rings.RingClosureParameters.ringClosabCondAsSMARTS, denoptim.graph.rings.RingClosureParameters.ringSizeBias, denoptim.graph.rings.RingClosureParameters.selectFragsFromCC, denoptim.graph.rings.RingClosureParameters.serializeRCCs, and denoptim.programs.RunTimeParameters.verbosity.

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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 849 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 396 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 473 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
ringClosabCondAsSMARTSa 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 360 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
biasesthe 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 293 of file RingClosureParameters.java.

References denoptim.graph.rings.RingClosureParameters.ringSizeBias.

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

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Member Data Documentation

◆ buildChelatesMode

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

Flag activating procedures favoring formation of chelates.

Definition at line 61 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 230 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 49 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 223 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 122 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 107 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 117 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 97 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 91 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 70 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 102 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 112 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 147 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 159 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 215 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 210 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 204 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 85 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 alignement implies a dot product of -1.0.

Definition at line 154 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 134 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 196 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 56 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 190 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);
}
}
}
denoptim.graph.rings.RingClosureParameters.maxRingSize
int maxRingSize
Maximum size (number of atoms) in ring closing chain.
Definition: RingClosureParameters.java:97

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

Definition at line 165 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 76 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 237 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: