Parameters controlling execution of the fragmenter. More...

Inheritance diagram for denoptim.programs.fragmenter.FragmenterParameters:

Collaboration diagram for denoptim.programs.fragmenter.FragmenterParameters:

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

int	getNumTasks ()

void	setNumTasks (int numParallelTasks)
	Sets the number of parallel tasks to run. More...

String	getStructuresFile ()

void	setStructuresFile (String structuresFile)
	Sets the pathname of the file containing input structures. More...

void	setFormulaeFile (String formulaeFile)
	Sets the pathname of the file containing molecular formula with a format respecting Cambridge Structural Database format). More...

String	getFormulaeFile ()

List< CuttingRule >	getCuttingRules ()

void	setCuttingRules (List< CuttingRule > cuttingRules)
	Assigns the cutting rules loaded from the input. More...

void	setCuttingRulesFilePathname (String pathname)
	Assigns the pathname to the cutting rules file. More...

String	getCuttingRulesFilePathname ()

LinkedHashMap< String, String >	getFormulae ()

boolean	doCheckFormula ()

void	setCheckFormula (boolean checkFormula)
	Sets the value of the flag controlling the execution of elemental analysis on the structures. More...

boolean	doPreFilter ()

Set< String >	getPreFiltrationSMARTS ()

boolean	doFragmentation ()

boolean	doFragExtractionFromGraphs ()

boolean	doRejectWeirdIsotopes ()

boolean	doAddDuOnLinearity ()

Set< String >	getRejectedElements ()

Map< String, Double >	getRejectedFormulaLessThan ()

Set< Map< String, Double > >	getRejectedFormulaMoreThan ()

Set< String >	getRejectedAPClasses ()

Set< String[]>	getRejectedAPClassCombinations ()

int	getMaxFragHeavyAtomCount ()

int	getMinFragHeavyAtomCount ()

Map< String, String >	getFragRejectionSMARTS ()

Map< String, String >	getFragRetentionSMARTS ()

void	setRejectWeirdIsotopes (boolean doRejectWeirdIsotopes)

void	setRejectedElements (Set< String > rejectedElements)

void	setRejectedFormulaLessThan (Map< String, Double > formulaMax)

void	setRejectedFormulaMoreThan (Set< Map< String, Double > > formulaCriteriaMoreThan)

void	setRejectedAPClasses (Set< String > rejectedAPClasses)

void	setRejectedAPClassCombinations (Set< String[]> rejectedAPClassCombinations)

void	setMaxFragHeavyAtomCount (int maxFragHeavyAtomCount)

void	setMinFragHeavyAtomCount (int minFragHeavyAtomCount)

void	setFragRejectionSMARTS (Map< String, String > fragRejectionSMARTS)

void	setFragRetentionSMARTS (Map< String, String > fragRetentionSMARTS)

ArrayList< Vertex >	getIgnorableFragments ()

ArrayList< Vertex >	getTargetFragments ()

boolean	doManageIsomorphicFamilies ()

int	getIsomorphicSampleSize ()

void	setIsomorphicSampleSize (int isomorphicSampleSize)

int	getMWSlotSize ()

void	setMWSlotSize (int mwSlotSize)

Map< String, File >	getMWSlotToAllFragsFile ()

void	setMWSlotToAllFragsFile (Map< String, File > mwSlotToAllFragsFile)

Map< String, File >	getMWSlotToUnqFragsFile ()

File	getMWSlotFileNameUnqFrags (String mwSlotId)
	Builds the pathname of the file meant to hold unique fragments from within a given MW slot, i.e., holding the unique version of isomorphic fragment families. More...

File	getMWSlotFileNameAllFrags (String mwSlotId)
	Builds the pathname of the file meant to hold all isomorphic fragments from a given MW slot. More...

Map< String, Integer >	getIsomorphsCount ()

String	newIsomorphicFamilyID ()
	Produced a new unique identifier for a family of isomorphic fragments. More...

boolean	doFiltering ()

boolean	addExplicitH ()

void	setAddExplicitH (boolean addExplicitH)
	Give `true` to add explicit H atoms on all atoms. More...

boolean	acceptUnsetToSingeBO ()

void	setEmbedRingsInTemplate (boolean embedRingsInTemplate)

boolean	embedRingsInTemplate ()

void	setEmbeddedRingsContract (ContractLevel embeddedRingsContract)

ContractLevel	getEmbeddedRingsContract ()

void	setScaffoldingPolicy (ScaffoldingPolicy sp)

ScaffoldingPolicy	getScaffoldingPolicy ()

List< DGraph >	getFragmentationTmpls ()

int	getMaxBufferShellSize ()

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

List< CuttingRule >	getDefaultCuttingRules () throws IOException, DENOPTIMException
	Get default cutting rules from the class loader of the current class. More...

List< CuttingRule >	getDefaultCuttingRules (ClassLoader classLoader) throws IOException, DENOPTIMException
	Get default cutting rules from a given class loader. 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...

double	getLinearAngleLimit ()

void	setLinearAngleLimit (double linearAngleLimit)
	Sets the upper limit for an angle before it is treated as "flat" angle, i.e., close enough to 180 DEG. More...

boolean	doExtactRepresentativeConformer ()

int	getSizeUnimodalPop ()

void	setSizeUnimodalPop (int sizeUnimodalPop)
	Sets the size of the population of normally distributed noise-distorted population used to define the threshold RMSD of a unimodal distribution of geometric distortions. More...

double	getMaxNoiseUnimodalPop ()

void	setMaxNoiseUnimodalPop (double maxNoiseUnimodalPop)
	Sets the maximum noise of the population of normally distributed noise-distorted population used to define the threshold RMSD of a unimodal distribution of geometric distortions. More...

double	getFactorForSDOnStatsOfUnimodalPop ()

void	setFactorForSDOnStatsOfUnimodalPop (double factorForSDOnStatsOfUnimodalPop)
	Sets the weight of the standard deviation when calculating the RMSD threshold from the statistics of the RMSD over the population of normally distributed noise-distorted points with unimodal distribution of geometric distortions. More...

boolean	isUseCentroidsAsRepresentativeConformer ()

void	setUseCentroidsAsRepresentativeConformer (boolean useCentroidsAsRepresentativeConformer)

boolean	isSaveClustersOfConformerToFile ()

void	setSaveClustersOfConformerToFile (boolean saveClustersOfConformerToFile)
	Sets the flag requesting to print clusters of fragments to file upon extraction of the most representative conformers. More...

boolean	isStandaloneFragmentClustering ()

boolean	isWorkingIn3D ()

void	setWorkingIn3D (boolean workingIn3D)
	Sets boolean variable workingIn3D. More...

void	setFragmentationTmpls (List< DGraph > fragmentationTmpls)
	Sets the list of graph templates for fragmentation. 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
final Object	MANAGEMWSLOTSSLOCK = new Object()
	Synchronization lock for manipulating a) the collections (i.e., MW slots) of fragments produced by multiple threads and b) the relative information (i.e., isomorphic family size). More...

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

Static Public Attributes
static final int	MAXISOMORPHICSAMPLESIZE = 50
	Maximum isomorphic sample size. More...

Protected Attributes
boolean	embedRingsInTemplate = false
	Flag that enables the embedding of rings in templates upon conversion of molecules into `DGraph`. More...

ContractLevel	embeddedRingsContract = ContractLevel.FREE
	Type of constrain defined for any template generated upon conversion of molecules into `DGraph`. 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...

Package Attributes
List< CuttingRule >	cuttingRules
	List of cutting rules sorted by priority. More...

Private Member Functions
void	createWorkingDirectory ()

Private Attributes
String	structuresFile
	Pathname to the file containing the structures of the molecules to fragment or the fragments to process. More...

String	formulaeFile
	Pathname to the file containing the formulae of the molecules to fragment. More...

LinkedHashMap< String, String >	formulae
	Molecular formula read-in from CSD file. More...

String	cutRulesFile
	Pathname to the file containing the cutting rules. More...

int	numParallelTasks = 1
	Number of parallel tasks to run. More...

boolean	doCheckFormula = false
	Flag requesting the execution of elemental analysis and comparison of the content of the structure file against a given molecular formula. More...

boolean	acceptUnsetToSingeBOApprox = false
	Flag requesting to force-accepting the approximation that converts all unset bond orders to single bond orders. More...

boolean	addExplicitH = false
	Flag requesting to add explicit H atoms. More...

boolean	doPreFilter = false
	Flag requesting the pre-fragmentation filtering of the structures. More...

Set< String >	preFilterSMARTS = new HashSet<String>()
	SMARTS identifying substructures that lead to rejection of a structure before fragmentation. More...

boolean	doFragmentation = false
	Flag requesting the fragmentation of the structures. More...

boolean	doFiltering = false
	Flag requesting to do post-fragmentation processing of fragments, i.e., application of all filtration and rejection rules that can be applied after fragmentation, though starting from an input that is already a collection of fragments. More...

boolean	doFragExtractionFromGraphs = false
	Flag requesting to extract fragments from graphs. More...

boolean	doRejectWeirdIsotopes = true
	Flag requesting to reject fragments with minor isotopes. More...

Set< String >	rejectedElements = new HashSet<String>()
	Symbols of elements that lead to rejection of a fragment. More...

Map< String, Double >	formulaCriteriaLessThan
	Lower limits of formula-based criteria for fragment rejection. More...

Set< Map< String, Double > >	formulaCriteriaMoreThan
	Upper limits of formula-based criteria for fragment rejection. More...

Set< String >	rejectedAPClasses = new HashSet<String>()
	The initial part of APClasses that lead to rejection of a fragment. More...

Set< String[]>	rejectedAPClassCombinations = new HashSet<String[]>()
	Combination of strings matching the beginning of APClass names that lead to rejection of a fragment. More...

int	maxFragHeavyAtomCount = -1
	Upper limit for number of non-H atoms in fragments. More...

int	minFragHeavyAtomCount = -1
	Lower limit for number of non-H atoms in fragments. More...

Map< String, String >	fragRejectionSMARTS = new HashMap<String, String>()
	SMARTS leading to rejection of a fragment. More...

Map< String, String >	fragRetentionSMARTS = new HashMap<String, String>()
	SMARTS leading to retention of a fragment. More...

boolean	doAddDuOnLinearity = true
	Flag requesting to add dummy atoms on linearities. More...

double	linearAngleLimit = 170.0
	Upper limit for an angle before it is treated as "flat" ("linear") angle, i.e., close enough to 180 DEG. More...

String	ignorableFragmentsFile = ""
	Pathname to file with fragments that can be ignored. More...

ArrayList< Vertex >	ignorableFragments = new ArrayList<Vertex>()
	List of fragment that can be rejected. More...

String	targetFragmentsFile = ""
	Pathname to file with fragments that will be retained, i.e., any isomorphic fragment of any of these will be kept, all the rest rejected. More...

ArrayList< Vertex >	targetFragments = new ArrayList<Vertex>()
	List of fragment that will be retained, i.e., any isomorphic fragment of any of these will be kept, all the rest rejected. More...

boolean	doManageIsomorphicFamilies = false

int	isomorphicSampleSize = 1
	Size of the sample of isomorphic fragments to collect. More...

int	mwSlotSize = 10
	Molecular weight slot width for collecting fragments. More...

Map< String, File >	mwSlotToAllFragsFile = new HashMap<String,File>()
	Mapping of the molecular weight slot identifier to the file collecting all collected fragments belonging to that MW slot. More...

Map< String, File >	mwSlotToUnqFragsFile = new HashMap<String,File>()
	Mapping of the molecular weight slot identifier to the file collecting unique fragments belonging to that MW slot. More...

Map< String, Integer >	isomorphsCount = new HashMap<String,Integer>()
	Counts of isomorphic versions of each known fragment generated in a fragmentation process. More...

AtomicInteger	unqIsomorphicFamilyId = new AtomicInteger(0)
	Unique identifier of a family of isomorphic versions of a fragment,. More...

boolean	doExtactRepresentativeConformer = false
	Flag signaling the request to analyze each isomorphic family to extract the most representative fragment and make it be the champion of that family. More...

int	sizeUnimodalPop = 20
	Size of on-the-fly generated, normally distributed noise-distorted population of geometries used to determine properties of unimodal population of distorted points around an N-dimensional point. More...

double	maxNoiseUnimodalPop = 0.2
	Maximum amount of absolute noise used to generate normally distributed noise-distorted population of points around an N-dimensional point. More...

double	factorForSDOnStatsOfUnimodalPop = 1.0
	Factor used to multiply the standard deviation when adding it to the mean of the RMSD for a unimodal population of distorted of points around an N-dimensional point, thus defining a threshold for deciding whether a query point belong to that population or not. More...

boolean	useCentroidsAsRepresentativeConformer = true
	Flag requesting to same cluster centroids rather than the actual fragments that are closest to the centroids. More...

boolean	saveClustersOfConformerToFile = false
	Flag requesting to print clusters of fragments to file. More...

boolean	isStandaloneFragmentClustering = false
	Flag requesting to run fragment clusterer in stand-alone fashion. More...

boolean	workingIn3D = true
	Flag activating operations depending on 3D structure. More...

ScaffoldingPolicy	scaffoldingPolicy
	The policy for defining the scaffold vertex in a graph that does not have such a `BBType`. More...

String	fragmentationTmplFile = ""
	Pathname to file containing a graph to be used as template for fragmentation. More...

List< DGraph >	fragmentationTmpls = new ArrayList<DGraph>()
	List of graphs to be used as templates for fragmentation. More...

int	maxBufferShellSize = 2
	Maximum number of buffer shells to consider for fragmentation. 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 controlling execution of the fragmenter.

Author: Marco Foscato

Definition at line 60 of file FragmenterParameters.java.

Constructor & Destructor Documentation

◆ FragmenterParameters()

denoptim.programs.fragmenter.FragmenterParameters.FragmenterParameters ( )

Constructor.

Definition at line 415 of file FragmenterParameters.java.

References denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS.

Member Function Documentation

◆ acceptUnsetToSingeBO()

boolean denoptim.programs.fragmenter.FragmenterParameters.acceptUnsetToSingeBO ( )

Returns: true if we are want to ignore the fact we have translated unset bond orders to single-order bonds.

Definition at line 989 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.acceptUnsetToSingeBOApprox.

Referenced by denoptim.fragmenter.FragmenterTools.prepareMolToFragmentation().

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◆ addExplicitH()

boolean denoptim.programs.fragmenter.FragmenterParameters.addExplicitH ( )

Returns: true if we are asked to add explicit H atoms.

Definition at line 967 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.addExplicitH.

◆ checkParameters()

void denoptim.programs.fragmenter.FragmenterParameters.checkParameters ( ) throws DENOPTIMException

Evaluate consistency of input parameters.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 1419 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.Fragmenter.runProgram(), and denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ createWorkingDirectory()

void denoptim.programs.fragmenter.FragmenterParameters.createWorkingDirectory ( )

private

Definition at line 1527 of file FragmenterParameters.java.

References denoptim.files.FileUtils.addToRecentFiles(), denoptim.files.FileUtils.createDirectory(), denoptim.files.FileFormat.FRG_RUN, denoptim.programs.RunTimeParameters.logFile, and denoptim.programs.RunTimeParameters.workDir.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.processParameters().

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◆ doAddDuOnLinearity()

boolean denoptim.programs.fragmenter.FragmenterParameters.doAddDuOnLinearity ( )

Returns: true if we want to add dummy atoms to resolve linearities in internal coordinates.

Definition at line 619 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doAddDuOnLinearity.

◆ doCheckFormula()

boolean denoptim.programs.fragmenter.FragmenterParameters.doCheckFormula ( )

Returns: true if we are asked to perform the comparison of each element (i.e., elemental analysis) present in the structure file (structuresFile) against that of a given molecular formula, which comes from the formulaeFile.

Definition at line 543 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doCheckFormula.

◆ doExtactRepresentativeConformer()

boolean denoptim.programs.fragmenter.FragmenterParameters.doExtactRepresentativeConformer ( )

Returns: true if we want to extract the most representative conformer from each isomorphic family.

Definition at line 1605 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doExtactRepresentativeConformer.

◆ doFiltering()

boolean denoptim.programs.fragmenter.FragmenterParameters.doFiltering ( )

Returns: true if we want to do post-processing (i.e., filter and reject or collect fragments) on a given list of fragments (i.e., the input), thus skipping any fragmentation.

Definition at line 957 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doFiltering.

◆ doFragExtractionFromGraphs()

boolean denoptim.programs.fragmenter.FragmenterParameters.doFragExtractionFromGraphs ( )

Returns: true if we are asked to extract fragments from graphs.

Definition at line 597 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doFragExtractionFromGraphs.

◆ doFragmentation()

boolean denoptim.programs.fragmenter.FragmenterParameters.doFragmentation ( )

Returns: true if we are asked to fragment structures.

Definition at line 587 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doFragmentation.

◆ doManageIsomorphicFamilies()

boolean denoptim.programs.fragmenter.FragmenterParameters.doManageIsomorphicFamilies ( )

One needs to manage isomorphic families, i.e., manage duplicate fragments if we want to identify isomorphic fragments and keep only one isomorphic fragment (i.e., remove all duplicate fragments), or more then more isomorphic fragment. In the latter case, we essentially want to sample the isomorphic family. The extent of this, i.e., the size of the sample is controlled by isomorphicSampleSize).

Also, if we run multiple threads and want to remove duplicate fragments , each of thread may generate a new fragment that the others have not yet found. Thus, the existence of the new fragment must be communicated to the other threads avoiding concurrent generation of the same fragment from different threads.

The management of isomorphic families involves:

Splitting fragments according to molecular weight (MW) to limit the operations on the list of fragments to a small portion of the entire list of fragments.
Separate collection of unique versions of a fragment (the first found) and of the sample of the family of fragments isomorphic to the first.
Thread-safe manipulation of the two MW-split collections: the unique, and the family sample.
Unification of the MW-split collections to obtain the overall result.

Returns: true if we need to manage isomorphic families.

Definition at line 840 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doManageIsomorphicFamilies.

◆ doPreFilter()

boolean denoptim.programs.fragmenter.FragmenterParameters.doPreFilter ( )

Returns: true if we are asked to filter initial structures.

Definition at line 566 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doPreFilter.

◆ doRejectWeirdIsotopes()

boolean denoptim.programs.fragmenter.FragmenterParameters.doRejectWeirdIsotopes ( )

Returns: true if we want to remove fragments that contain isotopes that are not the major isotope for that element.

Definition at line 608 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doRejectWeirdIsotopes.

◆ embedRingsInTemplate()

boolean denoptim.programs.fragmenter.FragmenterParameters.embedRingsInTemplate ( )

Returns: the flag that enables the embedding of rings in templates upon conversion of molecules into DGraph .

Definition at line 1011 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.embedRingsInTemplate.

◆ getCuttingRules()

List< CuttingRule > denoptim.programs.fragmenter.FragmenterParameters.getCuttingRules ( )

Returns: the cutting rules currently configured in this set of parameters.

Definition at line 490 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.cuttingRules.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.programs.mol2graph.Mol2GraphParameters.getCuttingRules(), denoptim.gui.GUIVertexInspector.initialize(), and denoptim.programs.mol2graph.Mol2GraphParameters.processParameters().

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◆ getCuttingRulesFilePathname()

String denoptim.programs.fragmenter.FragmenterParameters.getCuttingRulesFilePathname ( )

Returns: the pathname to the cutting rules file.

Definition at line 520 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.cutRulesFile.

Referenced by denoptim.gui.GUIVertexInspector.dialogToDefineCuttingRules(), denoptim.gui.GUIGraphHandler.initialize(), and denoptim.gui.GUIVertexInspector.initialize().

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◆ getDefaultCuttingRules() [1/2]

List< CuttingRule > denoptim.programs.fragmenter.FragmenterParameters.getDefaultCuttingRules ( ) throws IOException, DENOPTIMException

Get default cutting rules from the class loader of the current class.

Definition at line 1385 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.getDefaultCuttingRules().

Referenced by denoptim.gui.GUIVertexInspector.dialogToDefineCuttingRules(), denoptim.programs.fragmenter.FragmenterParameters.getDefaultCuttingRules(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

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◆ getDefaultCuttingRules() [2/2]

List< CuttingRule > denoptim.programs.fragmenter.FragmenterParameters.getDefaultCuttingRules ( ClassLoader classLoader ) throws IOException, DENOPTIMException

Get default cutting rules from a given class loader.

Definition at line 1395 of file FragmenterParameters.java.

References denoptim.io.DenoptimIO.readCuttingRules().

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◆ getEmbeddedRingsContract()

ContractLevel denoptim.programs.fragmenter.FragmenterParameters.getEmbeddedRingsContract ( )

Returns: the type of constrain defined for any template generated upon conversion of molecules into DGraph.

Definition at line 1034 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.embeddedRingsContract.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), and denoptim.programs.mol2graph.Mol2GraphParameters.getEmbeddedRingsContract().

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◆ getFactorForSDOnStatsOfUnimodalPop()

double denoptim.programs.fragmenter.FragmenterParameters.getFactorForSDOnStatsOfUnimodalPop ( )

Returns: the weight of the standard deviation when calculating the RMSD threshold from the statistics of the RMSD over the population of normally distributed noise-distorted points with unimodal distribution of geometric distortions.

Definition at line 1668 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.factorForSDOnStatsOfUnimodalPop.

Referenced by denoptim.fragmenter.FragmentClusterer.mergeClusters().

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◆ getFormulae()

LinkedHashMap< String, String > denoptim.programs.fragmenter.FragmenterParameters.getFormulae ( )

Returns: the list of molecular formulae read-in from text file.

Definition at line 530 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.formulae.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads().

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◆ getFormulaeFile()

String denoptim.programs.fragmenter.FragmenterParameters.getFormulaeFile ( )

Returns: the pathname to the file containing the molecular formulae to work with.

Definition at line 480 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.formulaeFile.

◆ getFragmentationTmpls()

List< DGraph > denoptim.programs.fragmenter.FragmenterParameters.getFragmentationTmpls ( )

Returns: the graph to be used as template for fragmentation. If not set, no template will be used.

Definition at line 1067 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.fragmentationTmpls.

Referenced by denoptim.gui.GUIVertexInspector.initialize().

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◆ getFragRejectionSMARTS()

Map< String, String > denoptim.programs.fragmenter.FragmenterParameters.getFragRejectionSMARTS ( )

Returns: the SMARTS that lead to rejection of a fragment.

Definition at line 701 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.fragRejectionSMARTS.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getFragRetentionSMARTS()

Map< String, String > denoptim.programs.fragmenter.FragmenterParameters.getFragRetentionSMARTS ( )

Returns: the SMARTS that lead to retention of a fragment.

Definition at line 711 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.fragRetentionSMARTS.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getIgnorableFragments()

ArrayList< Vertex > denoptim.programs.fragmenter.FragmenterParameters.getIgnorableFragments ( )

Returns: list of fragment that can be rejected.

Definition at line 794 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.ignorableFragments.

◆ getIsomorphicSampleSize()

int denoptim.programs.fragmenter.FragmenterParameters.getIsomorphicSampleSize ( )

Definition at line 847 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.isomorphicSampleSize.

◆ getIsomorphsCount()

Map< String, Integer > denoptim.programs.fragmenter.FragmenterParameters.getIsomorphsCount ( )

Returns: the counts of isomorphic versions of each fragment.

Definition at line 934 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.isomorphsCount.

◆ getLinearAngleLimit()

double denoptim.programs.fragmenter.FragmenterParameters.getLinearAngleLimit ( )

Returns: the upper limit for an angle before it is treated as "flat" angle, i.e., close enough to 180 DEG.

Definition at line 1582 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.linearAngleLimit.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.gui.CuttingRulesSelectionDialog.CuttingRulesSelectionDialog(), denoptim.programs.mol2graph.Mol2GraphParameters.getLinearAngleLimit(), and denoptim.gui.GUIVertexInspector.initialize().

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◆ getMaxBufferShellSize()

int denoptim.programs.fragmenter.FragmenterParameters.getMaxBufferShellSize ( )

Returns: the maximum number of bonds to consider for including atoms around topology-critical atoms when trying to find a unique mapping between the template graph and the molecular structure.

Definition at line 1079 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.maxBufferShellSize.

Referenced by denoptim.gui.GUIVertexInspector.initialize().

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◆ getMaxFragHeavyAtomCount()

int denoptim.programs.fragmenter.FragmenterParameters.getMaxFragHeavyAtomCount ( )

Returns: the max number of heavy atoms to retain a fragment.

Definition at line 681 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.maxFragHeavyAtomCount.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getMaxNoiseUnimodalPop()

double denoptim.programs.fragmenter.FragmenterParameters.getMaxNoiseUnimodalPop ( )

Returns: the maximum noise of the population of normally distributed noise-distorted population used to define the threshold RMSD of a unimodal distribution of geometric distortions.

Definition at line 1642 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.maxNoiseUnimodalPop.

Referenced by denoptim.fragmenter.FragmentClusterer.mergeClusters().

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◆ getMinFragHeavyAtomCount()

int denoptim.programs.fragmenter.FragmenterParameters.getMinFragHeavyAtomCount ( )

Returns: the min number of heavy atoms to retain a fragment.

Definition at line 691 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.minFragHeavyAtomCount.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getMWSlotFileNameAllFrags()

File denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameAllFrags ( String mwSlotId )

Builds the pathname of the file meant to hold all isomorphic fragments from a given MW slot.

Parameters

mwSlotId the identifier of the MW slot.

Returns: the file collecting all isomorphic fragment families in the MW range of interest.

Definition at line 921 of file FragmenterParameters.java.

References denoptim.io.DenoptimIO.FS, denoptim.files.FileFormat.getExtension(), denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.constants.DENOPTIMConstants.MWSLOTFRAGSALLFILENANEEND, denoptim.constants.DENOPTIMConstants.MWSLOTFRAGSFILENAMEROOT, and denoptim.constants.DENOPTIMConstants.TMPFRAGFILEFORMAT.

Referenced by denoptim.fragmenter.ConformerExtractorTask.ConformerExtractorTask().

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◆ getMWSlotFileNameUnqFrags()

File denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameUnqFrags ( String mwSlotId )

Builds the pathname of the file meant to hold unique fragments from within a given MW slot, i.e., holding the unique version of isomorphic fragment families.

Parameters

mwSlotId the identifier of the MW slot.

Returns: the file collecting the unique version of isomorphic fragment families in the MW range of interest.

Definition at line 904 of file FragmenterParameters.java.

References denoptim.io.DenoptimIO.FS, denoptim.files.FileFormat.getExtension(), denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.constants.DENOPTIMConstants.MWSLOTFRAGSFILENAMEROOT, denoptim.constants.DENOPTIMConstants.MWSLOTFRAGSUNQFILENANEEND, and denoptim.constants.DENOPTIMConstants.TMPFRAGFILEFORMAT.

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◆ getMWSlotSize()

int denoptim.programs.fragmenter.FragmenterParameters.getMWSlotSize ( )

Definition at line 861 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.mwSlotSize.

Referenced by denoptim.fragmenter.ConformerExtractorTask.ConformerExtractorTask().

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◆ getMWSlotToAllFragsFile()

Map< String, File > denoptim.programs.fragmenter.FragmenterParameters.getMWSlotToAllFragsFile ( )

Definition at line 875 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.mwSlotToAllFragsFile.

◆ getMWSlotToUnqFragsFile()

Map< String, File > denoptim.programs.fragmenter.FragmenterParameters.getMWSlotToUnqFragsFile ( )

Definition at line 889 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.mwSlotToUnqFragsFile.

◆ getNumTasks()

int denoptim.programs.fragmenter.FragmenterParameters.getNumTasks ( )

Returns: the number of parallel tasks to run. Default is 1.

Definition at line 425 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.numParallelTasks.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.fragmenter.ParallelFragmentationAlgorithm.createAndSubmitTasks(), denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations(), denoptim.fragmenter.ParallelFragmentationAlgorithm.doPreFlightOperations(), denoptim.fragmenter.ParallelConformerExtractionAlgorithm.ParallelConformerExtractionAlgorithm(), denoptim.fragmenter.ParallelFragmentationAlgorithm.ParallelFragmentationAlgorithm(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads().

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◆ getPreFiltrationSMARTS()

Set< String > denoptim.programs.fragmenter.FragmenterParameters.getPreFiltrationSMARTS ( )

Returns: the SMARTS queries identifying substructures that lead to rejection of a structure before fragmentation.

Definition at line 577 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.preFilterSMARTS.

Referenced by denoptim.fragmenter.FragmenterTask.call().

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◆ getPrintedList()

String denoptim.programs.fragmenter.FragmenterParameters.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 1551 of file FragmenterParameters.java.

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

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◆ getRejectedAPClassCombinations()

Set< String[]> denoptim.programs.fragmenter.FragmenterParameters.getRejectedAPClassCombinations ( )

Returns: the combinations of classes leading to rejection of a fragment.

Definition at line 671 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.rejectedAPClassCombinations.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getRejectedAPClasses()

Set< String > denoptim.programs.fragmenter.FragmenterParameters.getRejectedAPClasses ( )

Returns: the classes leading to rejection of a fragment.

Definition at line 661 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.rejectedAPClasses.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getRejectedElements()

Set< String > denoptim.programs.fragmenter.FragmenterParameters.getRejectedElements ( )

Returns: the elemental symbols leading to rejection of a fragment.

Definition at line 629 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.rejectedElements.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getRejectedFormulaLessThan()

Map< String, Double > denoptim.programs.fragmenter.FragmenterParameters.getRejectedFormulaLessThan ( )

Returns: the formula-based criteria to reject a fragment if there are too few atoms of a certain element.

Definition at line 640 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.formulaCriteriaLessThan.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getRejectedFormulaMoreThan()

Set< Map< String, Double > > denoptim.programs.fragmenter.FragmenterParameters.getRejectedFormulaMoreThan ( )

Returns: the formula-based criteria to reject a fragment if there are too many atoms of a certain element.

Definition at line 651 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.formulaCriteriaMoreThan.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ getScaffoldingPolicy()

ScaffoldingPolicy denoptim.programs.fragmenter.FragmenterParameters.getScaffoldingPolicy ( )

Returns: the policy for defining the scaffold vertex in a graph that does not have such a BBType.

Definition at line 1056 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.scaffoldingPolicy.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), and denoptim.programs.mol2graph.Mol2GraphParameters.getScaffoldingPolicy().

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◆ getSizeUnimodalPop()

int denoptim.programs.fragmenter.FragmenterParameters.getSizeUnimodalPop ( )

Returns: the size of the population of normally distributed noise-distorted population used to define the threshold RMSD of a unimodal distribution of geometric distortions.

Definition at line 1617 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.sizeUnimodalPop.

Referenced by denoptim.fragmenter.FragmentClusterer.mergeClusters().

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◆ getStructuresFile()

String denoptim.programs.fragmenter.FragmenterParameters.getStructuresFile ( )

Returns: the pathname to the file containing the structures to work with.

Definition at line 446 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.structuresFile.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithm.doPreFlightOperations(), denoptim.programs.fragmenter.Fragmenter.runProgram(), denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads(), and denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ getTargetFragments()

ArrayList< Vertex > denoptim.programs.fragmenter.FragmenterParameters.getTargetFragments ( )

Returns: the list of fragment that will be retained, i.e., any isomorphic fragment of any of these will be kept, all the rest rejected.

Definition at line 805 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.targetFragments.

◆ interpretKeyword()

void denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword	(	String	key,
		String	value
	)		throws DENOPTIMException

Processes a keyword/value pair and assign the related parameters.

Parameters

key	the keyword as string
value	the value as a string

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 1092 of file FragmenterParameters.java.

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◆ isSaveClustersOfConformerToFile()

boolean denoptim.programs.fragmenter.FragmenterParameters.isSaveClustersOfConformerToFile ( )

Returns: true if we are asked to print clusters of fragments to file upon extraction of the most representative conformers.

Definition at line 1724 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.saveClustersOfConformerToFile.

Referenced by denoptim.fragmenter.ConformerExtractorTask.call().

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◆ isStandaloneFragmentClustering()

boolean denoptim.programs.fragmenter.FragmenterParameters.isStandaloneFragmentClustering ( )

Returns: true if we are asked to run only the clustering of fragments from a given list of fragment.

Definition at line 1749 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.isStandaloneFragmentClustering.

◆ isUseCentroidsAsRepresentativeConformer()

boolean denoptim.programs.fragmenter.FragmenterParameters.isUseCentroidsAsRepresentativeConformer ( )

Returns: true if we are asked to save cluster centroids rather than the actual fragments that are closest to the centroids upon extraction of the most representative conformers.

Definition at line 1696 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.useCentroidsAsRepresentativeConformer.

Referenced by denoptim.fragmenter.ConformerExtractorTask.call().

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◆ isWorkingIn3D()

boolean denoptim.programs.fragmenter.FragmenterParameters.isWorkingIn3D ( )

Returns: true if we are dealing with 3D structures

Definition at line 1760 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.workingIn3D.

Referenced by denoptim.fragmenter.FragmenterTools.filterFragment().

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◆ newIsomorphicFamilyID()

String denoptim.programs.fragmenter.FragmenterParameters.newIsomorphicFamilyID ( )

Produced a new unique identifier for a family of isomorphic fragments.

Returns: the unique ID.

Definition at line 945 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.unqIsomorphicFamilyId.

◆ processParameters()

void denoptim.programs.fragmenter.FragmenterParameters.processParameters ( ) throws DENOPTIMException

Processes all parameters and initialize related objects.

Exceptions

DENOPTIMException

Reimplemented from denoptim.programs.RunTimeParameters.

Definition at line 1446 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.Fragmenter.runProgram(), and denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ setAddExplicitH()

void denoptim.programs.fragmenter.FragmenterParameters.setAddExplicitH ( boolean addExplicitH )

Give true to add explicit H atoms on all atoms.

Useful, when importing molecules with implicit H notation.

Definition at line 978 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.addExplicitH.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule().

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◆ setCheckFormula()

void denoptim.programs.fragmenter.FragmenterParameters.setCheckFormula ( boolean checkFormula )

Sets the value of the flag controlling the execution of elemental analysis on the structures.

Parameters

checkFormula use true to request the elemental analysis.

Definition at line 555 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ setCuttingRules()

void denoptim.programs.fragmenter.FragmenterParameters.setCuttingRules ( List< CuttingRule > cuttingRules )

Assigns the cutting rules loaded from the input.

Definition at line 500 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.cuttingRules.

Referenced by denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.programs.mol2graph.Mol2GraphParameters.processParameters(), and denoptim.gui.CuttingRulesSelectionDialog.saveResults().

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◆ setCuttingRulesFilePathname()

void denoptim.programs.fragmenter.FragmenterParameters.setCuttingRulesFilePathname ( String pathname )

Assigns the pathname to the cutting rules file.

Definition at line 510 of file FragmenterParameters.java.

Referenced by denoptim.gui.CuttingRulesSelectionDialog.saveResults().

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◆ setEmbeddedRingsContract()

void denoptim.programs.fragmenter.FragmenterParameters.setEmbeddedRingsContract ( ContractLevel embeddedRingsContract )

Parameters

embeddedRingsContract the type of constrain defined for any template generated upon conversion of molecules into DGraph.

Definition at line 1023 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.embeddedRingsContract.

Referenced by denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.gui.MolToGraphParametersDialog.saveResults().

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◆ setEmbedRingsInTemplate()

void denoptim.programs.fragmenter.FragmenterParameters.setEmbedRingsInTemplate ( boolean embedRingsInTemplate )

Parameters

embedRingsInTemplate the flag that enables the embedding of rings in templates upon conversion of molecules into DGraph .

Definition at line 1000 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.embedRingsInTemplate.

Referenced by denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.gui.MolToGraphParametersDialog.saveResults().

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◆ setFactorForSDOnStatsOfUnimodalPop()

void denoptim.programs.fragmenter.FragmenterParameters.setFactorForSDOnStatsOfUnimodalPop ( double factorForSDOnStatsOfUnimodalPop )

Sets the weight of the standard deviation when calculating the RMSD threshold from the statistics of the RMSD over the population of normally distributed noise-distorted points with unimodal distribution of geometric distortions.

Definition at line 1682 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.factorForSDOnStatsOfUnimodalPop.

◆ setFormulaeFile()

void denoptim.programs.fragmenter.FragmenterParameters.setFormulaeFile ( String formulaeFile )

Sets the pathname of the file containing molecular formula with a format respecting Cambridge Structural Database format).

Parameters

formulaeFile

Definition at line 469 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.formulaeFile.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ setFragmentationTmpls()

void denoptim.programs.fragmenter.FragmenterParameters.setFragmentationTmpls ( List< DGraph > fragmentationTmpls )

Sets the list of graph templates for fragmentation.

Parameters

fragmentationTmpls the list of graph templates for fragmentation.

Definition at line 1782 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.fragmentationTmpls.

Referenced by denoptim.gui.GUIVertexInspector.initialize().

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◆ setFragRejectionSMARTS()

void denoptim.programs.fragmenter.FragmenterParameters.setFragRejectionSMARTS ( Map< String, String > fragRejectionSMARTS )

Definition at line 777 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.fragRejectionSMARTS.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setFragRetentionSMARTS()

void denoptim.programs.fragmenter.FragmenterParameters.setFragRetentionSMARTS ( Map< String, String > fragRetentionSMARTS )

Definition at line 784 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.fragRetentionSMARTS.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setIsomorphicSampleSize()

void denoptim.programs.fragmenter.FragmenterParameters.setIsomorphicSampleSize ( int isomorphicSampleSize )

Definition at line 854 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.isomorphicSampleSize.

◆ setLinearAngleLimit()

void denoptim.programs.fragmenter.FragmenterParameters.setLinearAngleLimit ( double linearAngleLimit )

Sets the upper limit for an angle before it is treated as "flat" angle, i.e., close enough to 180 DEG.

Parameters

linearAngleLimit the new value.

Definition at line 1594 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.linearAngleLimit.

Referenced by denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.gui.CuttingRulesSelectionDialog.saveResults().

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◆ setMaxFragHeavyAtomCount()

void denoptim.programs.fragmenter.FragmenterParameters.setMaxFragHeavyAtomCount ( int maxFragHeavyAtomCount )

Definition at line 763 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.maxFragHeavyAtomCount.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setMaxNoiseUnimodalPop()

void denoptim.programs.fragmenter.FragmenterParameters.setMaxNoiseUnimodalPop ( double maxNoiseUnimodalPop )

Sets the maximum noise of the population of normally distributed noise-distorted population used to define the threshold RMSD of a unimodal distribution of geometric distortions.

Definition at line 1655 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.maxNoiseUnimodalPop.

◆ setMinFragHeavyAtomCount()

void denoptim.programs.fragmenter.FragmenterParameters.setMinFragHeavyAtomCount ( int minFragHeavyAtomCount )

Definition at line 770 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.minFragHeavyAtomCount.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setMWSlotSize()

void denoptim.programs.fragmenter.FragmenterParameters.setMWSlotSize ( int mwSlotSize )

Definition at line 868 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.mwSlotSize.

◆ setMWSlotToAllFragsFile()

void denoptim.programs.fragmenter.FragmenterParameters.setMWSlotToAllFragsFile ( Map< String, File > mwSlotToAllFragsFile )

Definition at line 882 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.mwSlotToAllFragsFile.

◆ setNumTasks()

void denoptim.programs.fragmenter.FragmenterParameters.setNumTasks ( int numParallelTasks )

Sets the number of parallel tasks to run.

Parameters

numParallelTasks

Definition at line 436 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.numParallelTasks.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ setRejectedAPClassCombinations()

void denoptim.programs.fragmenter.FragmenterParameters.setRejectedAPClassCombinations ( Set< String[]> rejectedAPClassCombinations )

Definition at line 755 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.rejectedAPClassCombinations.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setRejectedAPClasses()

void denoptim.programs.fragmenter.FragmenterParameters.setRejectedAPClasses ( Set< String > rejectedAPClasses )

Definition at line 748 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.rejectedAPClasses.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setRejectedElements()

void denoptim.programs.fragmenter.FragmenterParameters.setRejectedElements ( Set< String > rejectedElements )

Definition at line 725 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.rejectedElements.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setRejectedFormulaLessThan()

void denoptim.programs.fragmenter.FragmenterParameters.setRejectedFormulaLessThan ( Map< String, Double > formulaMax )

Definition at line 732 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setRejectedFormulaMoreThan()

void denoptim.programs.fragmenter.FragmenterParameters.setRejectedFormulaMoreThan ( Set< Map< String, Double > > formulaCriteriaMoreThan )

Definition at line 740 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.formulaCriteriaMoreThan.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setRejectWeirdIsotopes()

void denoptim.programs.fragmenter.FragmenterParameters.setRejectWeirdIsotopes ( boolean doRejectWeirdIsotopes )

Definition at line 718 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.doRejectWeirdIsotopes.

Referenced by denoptim.fragmenter.FragmenterToolsTest.testFilterFragment().

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◆ setSaveClustersOfConformerToFile()

void denoptim.programs.fragmenter.FragmenterParameters.setSaveClustersOfConformerToFile ( boolean saveClustersOfConformerToFile )

Sets the flag requesting to print clusters of fragments to file upon extraction of the most representative conformers.

Parameters

saveClustersOfConformerToFile use true to request printing clusters of fragments to file.

Definition at line 1737 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.saveClustersOfConformerToFile.

◆ setScaffoldingPolicy()

void denoptim.programs.fragmenter.FragmenterParameters.setScaffoldingPolicy ( ScaffoldingPolicy sp )

Parameters

sp	the policy for defining the scaffold vertex in a graph that does not have such a `BBType`.

Definition at line 1045 of file FragmenterParameters.java.

Referenced by denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), and denoptim.gui.MolToGraphParametersDialog.saveResults().

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◆ setSizeUnimodalPop()

void denoptim.programs.fragmenter.FragmenterParameters.setSizeUnimodalPop ( int sizeUnimodalPop )

Sets the size of the population of normally distributed noise-distorted population used to define the threshold RMSD of a unimodal distribution of geometric distortions.

Definition at line 1629 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.sizeUnimodalPop.

◆ setStructuresFile()

void denoptim.programs.fragmenter.FragmenterParameters.setStructuresFile ( String structuresFile )

Sets the pathname of the file containing input structures.

Parameters

structuresFile the pathname.

Definition at line 457 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.structuresFile.

Referenced by denoptim.fragmenter.ParallelFragmentationAlgorithmTest.testSplitInputForThreads().

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◆ setUseCentroidsAsRepresentativeConformer()

void denoptim.programs.fragmenter.FragmenterParameters.setUseCentroidsAsRepresentativeConformer ( boolean useCentroidsAsRepresentativeConformer )

Parameters

useCentroidsAsRepresentativeConformer set to true to request saving cluster centroids rather than the actual fragments that are closest to the centroids upon extraction of the most representative conformers.

Definition at line 1710 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.useCentroidsAsRepresentativeConformer.

◆ setWorkingIn3D()

void denoptim.programs.fragmenter.FragmenterParameters.setWorkingIn3D ( boolean workingIn3D )

Sets boolean variable workingIn3D.

Parameters

workingIn3D

Definition at line 1771 of file FragmenterParameters.java.

References denoptim.programs.fragmenter.FragmenterParameters.workingIn3D.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.fragmenter.ParallelFragmentationAlgorithm.doPreFlightOperations(), and denoptim.ga.EvolutionaryAlgorithm.initializePopulation().

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Member Data Documentation

◆ acceptUnsetToSingeBOApprox

boolean denoptim.programs.fragmenter.FragmenterParameters.acceptUnsetToSingeBOApprox = false

private

Flag requesting to force-accepting the approximation that converts all unset bond orders to single bond orders.

This to signify 'a bond exist' between atoms for which there is no proper bond order. Still, considerations based on evaluating the bond order will be misguided.

Definition at line 108 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.acceptUnsetToSingeBO(), and denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword().

◆ addExplicitH

boolean denoptim.programs.fragmenter.FragmenterParameters.addExplicitH = false

private

Flag requesting to add explicit H atoms.

Definition at line 113 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.addExplicitH(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), denoptim.fragmenter.FragmenterTools.prepareMolToFragmentation(), and denoptim.programs.fragmenter.FragmenterParameters.setAddExplicitH().

◆ cutRulesFile

String denoptim.programs.fragmenter.FragmenterParameters.cutRulesFile

private

Pathname to the file containing the cutting rules.

Definition at line 83 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.getCuttingRulesFilePathname(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ cuttingRules

List<CuttingRule> denoptim.programs.fragmenter.FragmenterParameters.cuttingRules

package

List of cutting rules sorted by priority.

Definition at line 88 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getCuttingRules(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), and denoptim.programs.fragmenter.FragmenterParameters.setCuttingRules().

◆ doAddDuOnLinearity

boolean denoptim.programs.fragmenter.FragmenterParameters.doAddDuOnLinearity = true

private

Flag requesting to add dummy atoms on linearities.

This to enable 3D-modeling of the system with internal coordinates.

Definition at line 210 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.doAddDuOnLinearity().

◆ doCheckFormula

boolean denoptim.programs.fragmenter.FragmenterParameters.doCheckFormula = false

private

Flag requesting the execution of elemental analysis and comparison of the content of the structure file against a given molecular formula.

This task is meant to identify structures with missing atoms.

Definition at line 100 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.programs.fragmenter.FragmenterParameters.doCheckFormula(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads().

◆ doExtactRepresentativeConformer

boolean denoptim.programs.fragmenter.FragmenterParameters.doExtactRepresentativeConformer = false

private

Flag signaling the request to analyze each isomorphic family to extract the most representative fragment and make it be the champion of that family.

Definition at line 326 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.doExtactRepresentativeConformer(), denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ doFiltering

boolean denoptim.programs.fragmenter.FragmenterParameters.doFiltering = false

private

Flag requesting to do post-fragmentation processing of fragments, i.e., application of all filtration and rejection rules that can be applied after fragmentation, though starting from an input that is already a collection of fragments.

Essentially, skip fragmentation and filter the given fragments

Definition at line 139 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.programs.fragmenter.FragmenterParameters.doFiltering(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ doFragExtractionFromGraphs

boolean denoptim.programs.fragmenter.FragmenterParameters.doFragExtractionFromGraphs = false

private

Flag requesting to extract fragments from graphs.

Definition at line 144 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.programs.fragmenter.FragmenterParameters.doFragExtractionFromGraphs(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ doFragmentation

boolean denoptim.programs.fragmenter.FragmenterParameters.doFragmentation = false

private

Flag requesting the fragmentation of the structures.

Definition at line 130 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.programs.fragmenter.FragmenterParameters.doFragmentation(), denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ doManageIsomorphicFamilies

boolean denoptim.programs.fragmenter.FragmenterParameters.doManageIsomorphicFamilies = false

private

Flag signaling the need to manage isomorphic families, i.e., manage duplicate fragments. This is needed if we want to identify isomorphic fragments and keep only one isomorphic fragment (i.e., remove all duplicate fragments), or more then one isomorphic fragment. In the latter case, we essentially want to sample the isomorphic family. The extent of this, i.e., the size of the sample is controlled by isomorphicSampleSize).

Also, if we run multiple threads and want to remove duplicate fragments , each thread may generate a new fragment that the others have not yet found. Thus, the existence of the new fragment must be communicated to the other threads avoiding concurrent generation of the same fragment from different threads.

The management of isomorphic families involves:

Splitting fragments according to molecular weight (MW) to limit the operations on the list of fragments to a small portion of the entire list of fragments.
Separate collection of unique versions of a fragment (the first found) and of the sample of the family of fragments isomorphic to the first.
Thread-safe manipulation of the two MW-split collections: the unique, and the family sample.
Unification of the MW-split collections to obtain the overall result.

Definition at line 267 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.doManageIsomorphicFamilies(), denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ doPreFilter

boolean denoptim.programs.fragmenter.FragmenterParameters.doPreFilter = false

private

Flag requesting the pre-fragmentation filtering of the structures.

Definition at line 118 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.programs.fragmenter.FragmenterParameters.doPreFilter(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ doRejectWeirdIsotopes

boolean denoptim.programs.fragmenter.FragmenterParameters.doRejectWeirdIsotopes = true

private

Flag requesting to reject fragments with minor isotopes.

Definition at line 149 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.doRejectWeirdIsotopes(), denoptim.fragmenter.FragmenterTools.filterFragment(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setRejectWeirdIsotopes().

◆ embeddedRingsContract

ContractLevel denoptim.programs.fragmenter.FragmenterParameters.embeddedRingsContract = ContractLevel.FREE

protected

Type of constrain defined for any template generated upon conversion of molecules into DGraph.

Definition at line 391 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getEmbeddedRingsContract(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setEmbeddedRingsContract().

◆ embedRingsInTemplate

boolean denoptim.programs.fragmenter.FragmenterParameters.embedRingsInTemplate = false

protected

Flag that enables the embedding of rings in templates upon conversion of molecules into DGraph.

Definition at line 385 of file FragmenterParameters.java.

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.programs.fragmenter.FragmenterParameters.embedRingsInTemplate(), denoptim.programs.mol2graph.Mol2GraphParameters.embedRingsInTemplate(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setEmbedRingsInTemplate().

◆ factorForSDOnStatsOfUnimodalPop

double denoptim.programs.fragmenter.FragmenterParameters.factorForSDOnStatsOfUnimodalPop = 1.0

private

Factor used to multiply the standard deviation when adding it to the mean of the RMSD for a unimodal population of distorted of points around an N-dimensional point, thus defining a threshold for deciding whether a query point belong to that population or not.

Used by FragmentClusterer.

Definition at line 351 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getFactorForSDOnStatsOfUnimodalPop(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setFactorForSDOnStatsOfUnimodalPop().

◆ formulaCriteriaLessThan

Map<String,Double> denoptim.programs.fragmenter.FragmenterParameters.formulaCriteriaLessThan

private

Initial value:

=

new HashMap<String,Double>()

Lower limits of formula-based criteria for fragment rejection.

I.e., if a fragment has a formula that counts less then what defined here, it is rejected.

Definition at line 161 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getRejectedFormulaLessThan(), and denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword().

◆ formulaCriteriaMoreThan

Set<Map<String,Double> > denoptim.programs.fragmenter.FragmenterParameters.formulaCriteriaMoreThan

private

Initial value:

=

new HashSet<Map<String,Double>>()

Upper limits of formula-based criteria for fragment rejection.

I.e., if a fragment has a formula that counts more then what defined here, it is rejected.

Definition at line 169 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getRejectedFormulaMoreThan(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setRejectedFormulaMoreThan().

◆ formulae

LinkedHashMap<String, String> denoptim.programs.fragmenter.FragmenterParameters.formulae

private

Molecular formula read-in from CSD file.

Data collected by CSD refcode.

Definition at line 78 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getFormulae(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ formulaeFile

String denoptim.programs.fragmenter.FragmenterParameters.formulaeFile

private

Pathname to the file containing the formulae of the molecules to fragment.

Definition at line 72 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.getFormulaeFile(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), and denoptim.programs.fragmenter.FragmenterParameters.setFormulaeFile().

◆ fragmentationTmplFile

String denoptim.programs.fragmenter.FragmenterParameters.fragmentationTmplFile = ""

private

Pathname to file containing a graph to be used as template for fragmentation.

If not set, no template will be used.

Definition at line 397 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ fragmentationTmpls

List<DGraph> denoptim.programs.fragmenter.FragmenterParameters.fragmentationTmpls = new ArrayList<DGraph>()

private

List of graphs to be used as templates for fragmentation.

If not set, no template will be used.

Definition at line 403 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getFragmentationTmpls(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), and denoptim.programs.fragmenter.FragmenterParameters.setFragmentationTmpls().

◆ fragRejectionSMARTS

Map<String, String> denoptim.programs.fragmenter.FragmenterParameters.fragRejectionSMARTS = new HashMap<String, String>()

private

SMARTS leading to rejection of a fragment.

Definition at line 198 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getFragRejectionSMARTS(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setFragRejectionSMARTS().

◆ fragRetentionSMARTS

Map<String, String> denoptim.programs.fragmenter.FragmenterParameters.fragRetentionSMARTS = new HashMap<String, String>()

private

SMARTS leading to retention of a fragment.

All fragments not matching one of these are rejected.

Definition at line 204 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getFragRetentionSMARTS(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setFragRetentionSMARTS().

◆ ignorableFragments

ArrayList<Vertex> denoptim.programs.fragmenter.FragmenterParameters.ignorableFragments = new ArrayList<Vertex>()

private

List of fragment that can be rejected.

Definition at line 226 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getIgnorableFragments(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ ignorableFragmentsFile

String denoptim.programs.fragmenter.FragmenterParameters.ignorableFragmentsFile = ""

private

Pathname to file with fragments that can be ignored.

Definition at line 221 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ isomorphicSampleSize

int denoptim.programs.fragmenter.FragmenterParameters.isomorphicSampleSize = 1

private

Size of the sample of isomorphic fragments to collect.

When this number N is larger then one, we will collect the first N isomorphic forms of each fragment. A value of 1 corresponds to saying "remove all isomorphic duplicates".

Definition at line 275 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.getIsomorphicSampleSize(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setIsomorphicSampleSize().

◆ isomorphsCount

Map<String,Integer> denoptim.programs.fragmenter.FragmenterParameters.isomorphsCount = new HashMap<String,Integer>()

private

Counts of isomorphic versions of each known fragment generated in a fragmentation process.

The key is a string that identifies the vertex without having to hold the entire data structure of it.

Definition at line 304 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getIsomorphsCount().

◆ isStandaloneFragmentClustering

boolean denoptim.programs.fragmenter.FragmenterParameters.isStandaloneFragmentClustering = false

private

Flag requesting to run fragment clusterer in stand-alone fashion.

Definition at line 367 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.ConformerExtractorTask.call(), denoptim.programs.fragmenter.FragmenterParameters.isStandaloneFragmentClustering(), denoptim.programs.fragmenter.FragmenterParameters.processParameters(), and denoptim.programs.fragmenter.Fragmenter.runProgram().

◆ linearAngleLimit

double denoptim.programs.fragmenter.FragmenterParameters.linearAngleLimit = 170.0

private

Upper limit for an angle before it is treated as "flat" ("linear") angle, i.e., close enough to 180 DEG.

Definition at line 216 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getLinearAngleLimit(), and denoptim.programs.fragmenter.FragmenterParameters.setLinearAngleLimit().

◆ MANAGEMWSLOTSSLOCK

final Object denoptim.programs.fragmenter.FragmenterParameters.MANAGEMWSLOTSSLOCK = new Object()

Synchronization lock for manipulating a) the collections (i.e., MW slots) of fragments produced by multiple threads and b) the relative information (i.e., isomorphic family size).

Definition at line 319 of file FragmenterParameters.java.

◆ maxBufferShellSize

int denoptim.programs.fragmenter.FragmenterParameters.maxBufferShellSize = 2

private

Maximum number of buffer shells to consider for fragmentation.

Definition at line 408 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getMaxBufferShellSize(), and denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword().

◆ maxFragHeavyAtomCount

int denoptim.programs.fragmenter.FragmenterParameters.maxFragHeavyAtomCount = -1

private

Upper limit for number of non-H atoms in fragments.

Negative number is used to disable checking of the number of atoms.

Definition at line 187 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getMaxFragHeavyAtomCount(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setMaxFragHeavyAtomCount().

◆ MAXISOMORPHICSAMPLESIZE

final int denoptim.programs.fragmenter.FragmenterParameters.MAXISOMORPHICSAMPLESIZE = 50

static

Maximum isomorphic sample size.

Definition at line 280 of file FragmenterParameters.java.

Referenced by denoptim.fragmenter.ConformerExtractorTask.extractClusterableFragments().

◆ maxNoiseUnimodalPop

double denoptim.programs.fragmenter.FragmenterParameters.maxNoiseUnimodalPop = 0.2

private

Maximum amount of absolute noise used to generate normally distributed noise-distorted population of points around an N-dimensional point.

Used by FragmentClusterer.

Definition at line 341 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getMaxNoiseUnimodalPop(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setMaxNoiseUnimodalPop().

◆ minFragHeavyAtomCount

int denoptim.programs.fragmenter.FragmenterParameters.minFragHeavyAtomCount = -1

private

Lower limit for number of non-H atoms in fragments.

Negative number is used to disable checking of the number of atoms.

Definition at line 193 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getMinFragHeavyAtomCount(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setMinFragHeavyAtomCount().

◆ mwSlotSize

int denoptim.programs.fragmenter.FragmenterParameters.mwSlotSize = 10

private

Molecular weight slot width for collecting fragments.

Definition at line 285 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.getMWSlotSize(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setMWSlotSize().

◆ mwSlotToAllFragsFile

Map<String,File> denoptim.programs.fragmenter.FragmenterParameters.mwSlotToAllFragsFile = new HashMap<String,File>()

private

Mapping of the molecular weight slot identifier to the file collecting all collected fragments belonging to that MW slot.

Definition at line 291 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getMWSlotToAllFragsFile(), and denoptim.programs.fragmenter.FragmenterParameters.setMWSlotToAllFragsFile().

◆ mwSlotToUnqFragsFile

Map<String,File> denoptim.programs.fragmenter.FragmenterParameters.mwSlotToUnqFragsFile = new HashMap<String,File>()

private

Mapping of the molecular weight slot identifier to the file collecting unique fragments belonging to that MW slot.

Definition at line 297 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getMWSlotToUnqFragsFile().

◆ numParallelTasks

int denoptim.programs.fragmenter.FragmenterParameters.numParallelTasks = 1

private

Number of parallel tasks to run.

Definition at line 93 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.getNumTasks(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setNumTasks().

◆ preFilterSMARTS

Set<String> denoptim.programs.fragmenter.FragmenterParameters.preFilterSMARTS = new HashSet<String>()

private

SMARTS identifying substructures that lead to rejection of a structure before fragmentation.

I.e., structures matching any of these queries will not be fragmented.

Definition at line 125 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getPreFiltrationSMARTS(), and denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword().

◆ rejectedAPClassCombinations

Set<String[]> denoptim.programs.fragmenter.FragmenterParameters.rejectedAPClassCombinations = new HashSet<String[]>()

private

Combination of strings matching the beginning of APClass names that lead to rejection of a fragment.

Definition at line 181 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getRejectedAPClassCombinations(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setRejectedAPClassCombinations().

◆ rejectedAPClasses

Set<String> denoptim.programs.fragmenter.FragmenterParameters.rejectedAPClasses = new HashSet<String>()

private

The initial part of APClasses that lead to rejection of a fragment.

Definition at line 175 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getRejectedAPClasses(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setRejectedAPClasses().

◆ rejectedElements

Set<String> denoptim.programs.fragmenter.FragmenterParameters.rejectedElements = new HashSet<String>()

private

Symbols of elements that lead to rejection of a fragment.

Definition at line 154 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getRejectedElements(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setRejectedElements().

◆ saveClustersOfConformerToFile

boolean denoptim.programs.fragmenter.FragmenterParameters.saveClustersOfConformerToFile = false

private

Flag requesting to print clusters of fragments to file.

Definition at line 362 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), denoptim.programs.fragmenter.FragmenterParameters.isSaveClustersOfConformerToFile(), and denoptim.programs.fragmenter.FragmenterParameters.setSaveClustersOfConformerToFile().

◆ scaffoldingPolicy

ScaffoldingPolicy denoptim.programs.fragmenter.FragmenterParameters.scaffoldingPolicy

private

Initial value:

=

ScaffoldingPolicy.LARGEST_FRAGMENT

The policy for defining the scaffold vertex in a graph that does not have such a BBType.

Definition at line 378 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getScaffoldingPolicy(), and denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword().

◆ sizeUnimodalPop

int denoptim.programs.fragmenter.FragmenterParameters.sizeUnimodalPop = 20

private

Size of on-the-fly generated, normally distributed noise-distorted population of geometries used to determine properties of unimodal population of distorted points around an N-dimensional point.

Used by FragmentClusterer.

Definition at line 334 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getSizeUnimodalPop(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setSizeUnimodalPop().

◆ structuresFile

String denoptim.programs.fragmenter.FragmenterParameters.structuresFile

private

Pathname to the file containing the structures of the molecules to fragment or the fragments to process.

Definition at line 66 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.getStructuresFile(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.setStructuresFile().

◆ targetFragments

ArrayList<Vertex> denoptim.programs.fragmenter.FragmenterParameters.targetFragments = new ArrayList<Vertex>()

private

List of fragment that will be retained, i.e., any isomorphic fragment of any of these will be kept, all the rest rejected.

Definition at line 238 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.getTargetFragments(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ targetFragmentsFile

String denoptim.programs.fragmenter.FragmenterParameters.targetFragmentsFile = ""

private

Pathname to file with fragments that will be retained, i.e., any isomorphic fragment of any of these will be kept, all the rest rejected.

Definition at line 232 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.checkParameters(), denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), and denoptim.programs.fragmenter.FragmenterParameters.processParameters().

◆ unqIsomorphicFamilyId

AtomicInteger denoptim.programs.fragmenter.FragmenterParameters.unqIsomorphicFamilyId = new AtomicInteger(0)

private

Unique identifier of a family of isomorphic versions of a fragment,.

Definition at line 312 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.newIsomorphicFamilyID().

◆ useCentroidsAsRepresentativeConformer

boolean denoptim.programs.fragmenter.FragmenterParameters.useCentroidsAsRepresentativeConformer = true

private

Flag requesting to same cluster centroids rather than the actual fragments that are closest to the centroids.

Definition at line 357 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.interpretKeyword(), denoptim.programs.fragmenter.FragmenterParameters.isUseCentroidsAsRepresentativeConformer(), and denoptim.programs.fragmenter.FragmenterParameters.setUseCentroidsAsRepresentativeConformer().

◆ workingIn3D

boolean denoptim.programs.fragmenter.FragmenterParameters.workingIn3D = true

private

Flag activating operations depending on 3D structure.

Definition at line 372 of file FragmenterParameters.java.

Referenced by denoptim.programs.fragmenter.FragmenterParameters.isWorkingIn3D(), and denoptim.programs.fragmenter.FragmenterParameters.setWorkingIn3D().

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

/github/workspace/src/main/java/denoptim/programs/fragmenter/FragmenterParameters.java

Public Member Functions

Public Attributes

Static Public Attributes

Protected Attributes

Package Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FragmenterParameters()

Member Function Documentation

◆ acceptUnsetToSingeBO()

◆ addExplicitH()

◆ checkParameters()

◆ createWorkingDirectory()

◆ doAddDuOnLinearity()

◆ doCheckFormula()

◆ doExtactRepresentativeConformer()

◆ doFiltering()

◆ doFragExtractionFromGraphs()

◆ doFragmentation()

◆ doManageIsomorphicFamilies()

◆ doPreFilter()

◆ doRejectWeirdIsotopes()

◆ embedRingsInTemplate()

◆ getCuttingRules()

◆ getCuttingRulesFilePathname()

◆ getDefaultCuttingRules() [1/2]

◆ getDefaultCuttingRules() [2/2]

◆ getEmbeddedRingsContract()

◆ getFactorForSDOnStatsOfUnimodalPop()

◆ getFormulae()

◆ getFormulaeFile()

◆ getFragmentationTmpls()

◆ getFragRejectionSMARTS()

◆ getFragRetentionSMARTS()

◆ getIgnorableFragments()

◆ getIsomorphicSampleSize()

◆ getIsomorphsCount()

◆ getLinearAngleLimit()

◆ getMaxBufferShellSize()

◆ getMaxFragHeavyAtomCount()

◆ getMaxNoiseUnimodalPop()

◆ getMinFragHeavyAtomCount()

◆ getMWSlotFileNameAllFrags()

◆ getMWSlotFileNameUnqFrags()

◆ getMWSlotSize()

◆ getMWSlotToAllFragsFile()

◆ getMWSlotToUnqFragsFile()

◆ getNumTasks()

◆ getPreFiltrationSMARTS()

◆ getPrintedList()

◆ getRejectedAPClassCombinations()

◆ getRejectedAPClasses()

◆ getRejectedElements()

◆ getRejectedFormulaLessThan()

◆ getRejectedFormulaMoreThan()

◆ getScaffoldingPolicy()

◆ getSizeUnimodalPop()

◆ getStructuresFile()

◆ getTargetFragments()

◆ interpretKeyword()

◆ isSaveClustersOfConformerToFile()

◆ isStandaloneFragmentClustering()

◆ isUseCentroidsAsRepresentativeConformer()

◆ isWorkingIn3D()

◆ newIsomorphicFamilyID()

◆ processParameters()

◆ setAddExplicitH()

◆ setCheckFormula()

◆ setCuttingRules()

◆ setCuttingRulesFilePathname()

◆ setEmbeddedRingsContract()

◆ setEmbedRingsInTemplate()

◆ setFactorForSDOnStatsOfUnimodalPop()

◆ setFormulaeFile()

◆ setFragmentationTmpls()

◆ setFragRejectionSMARTS()

◆ setFragRetentionSMARTS()