denoptim.ga.EAUtils Class Reference

Helper methods for the genetic algorithm. More...

Collaboration diagram for denoptim.ga.EAUtils:

Classes
enum	CandidateSource
	A chosen method for generation of new Candidates. More...

Static Public Member Functions
static int	chooseNumberOfSitesToMutate (double[] multiSiteMutationProb, double hit)
	Takes a decision on how many sites to mutate on a candidate. More...
static CandidateSource	pickNewCandidateGenerationMode (double xoverWeight, double mutWeight, double newWeight, Randomizer randomizer)
	Takes a decision on which CandidateSource method to use for generating a new Candidate. More...
static Candidate	buildCandidateByFragmentingMolecule (IAtomContainer mol, Monitor mnt, GAParameters settings, int index) throws DENOPTIMException
	Generates a candidate by fragmenting a molecule and generating the graph that reconnects all fragments to reform the original molecule. More...
static DGraph	makeGraphFromFragmentationOfMol (IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy) throws DENOPTIMException
	Converts a molecule into a DGraph by fragmentation and re-assembling of the fragments. More...
static DGraph	makeGraphFromFragmentationOfMol (IAtomContainer mol, List< CuttingRule > cuttingRules, Logger logger, ScaffoldingPolicy scaffoldingPolicy, double linearAngleLimit) throws DENOPTIMException
	Converts a molecule into a DGraph by fragmentation and re-assembling of the fragments. More...
static void	outputPopulationDetails (Population population, String filename, GAParameters settings, boolean printpathNames) throws DENOPTIMException
	Write out summary for the current GA population. More...
static String	getPathNameToGenerationFolder (int genID, GAParameters settings)
static String	getPathNameToGenerationDetailsFile (int genID, GAParameters settings)
static String	getPathNameToFinalPopulationFolder (GAParameters settings)
static String	getPathNameToFinalPopulationDetailsFile (GAParameters settings)
static double	getGrowthProbabilityAtLevel (int level, int scheme, double lambda, double sigmaOne, double sigmaTwo)
	Calculates the probability of adding a fragment to the given level. More...
static double	getMolSizeProbability (DGraph graph, GAParameters settings)
	Calculated the probability of extending a graph based on the current size of the molecular representation contained in the graph and the given parameters. More...
static double	getMolSizeProbability (DGraph graph, int scheme, double lambda, double sigmaOne, double sigmaTwo)
	Calculated the probability of extending a graph based on the current size of the molecular representation contained in the graph and the given parameters. More...
static double	getProbability (double value, int scheme, double lambda, double sigmaOne, double sigmaTwo)
	Calculated a probability given parameters defining the shape of the probability function and a single input value. More...
static double	getGrowthByLevelProbability (int level, GAParameters settings)
	Calculates the probability of adding a fragment to the given level. More...
static double	getCrowdingProbability (AttachmentPoint ap, GAParameters settings)
	Calculated the probability of using and attachment point rooted on an atom that is holding other attachment points which have already been used. More...
static double	getCrowdingProbability (int crowdedness, GAParameters settings)
	Calculated the probability of using and attachment point rooted on an atom that is holding other attachment points which have already been used. More...
static int	getCrowdedness (AttachmentPoint ap)
	Calculate the current crowdedness of the given attachment point. More...
static int	getCrowdedness (AttachmentPoint ap, boolean ignoreFreeRCVs)
	Calculate the current crowdedness of the given attachment point. More...
static double	getCrowdingProbability (AttachmentPoint ap, int scheme, double lambda, double sigmaOne, double sigmaTwo)
	Calculated the probability of using and attachment point rooted on an atom that is holding other attachment points that have already been used. More...
static double	getCrowdingProbabilityForCrowdedness (int crowdedness, int scheme, double lambda, double sigmaOne, double sigmaTwo)
	Calculated the crowding probability for a given level of crowdedness. More...
static AttachmentPoint	searchForApSuitableToRingClosure (AttachmentPoint apA, SymmetricAPs symAPsA, GAParameters settings)

Static Protected Member Functions
static void	createFolderForGeneration (int genId, GAParameters settings)
	Creates a folder meant to hold all the data generated during a generation. More...
static Population	importInitialPopulation (SizeControlledSet uniqueIDsSet, GAParameters settings) throws DENOPTIMException, IOException
	Reads unique identifiers and initial population file according to the GAParameters. More...
static CandidateSource	chooseGenerationMethod (GAParameters settings)
	Choose one of the methods to make new Candidates. More...
static List< Candidate >	buildCandidatesByXOver (List< Candidate > eligibleParents, Population population, Monitor mnt, GAParameters settings) throws DENOPTIMException
	Generates a pair of new offspring by performing a crossover operation. More...
static Candidate	buildCandidateByXOver (List< Candidate > eligibleParents, Population population, Monitor mnt, GAParameters settings) throws DENOPTIMException
	Generates a new offspring by performing a crossover operation. More...
static Candidate	buildCandidateByXOver (List< Candidate > eligibleParents, Population population, Monitor mnt, int[] choiceOfParents, int choiceOfXOverSites, int choiceOfOffstring, GAParameters settings) throws DENOPTIMException
	Generates a new offspring by performing a crossover operation. More...
static List< Candidate >	buildCandidatesByXOver (List< Candidate > eligibleParents, Population population, Monitor mnt, int[] choiceOfParents, int choiceOfXOverSites, int choiceOfOffstring, GAParameters settings, int maxCandidatesToReturn) throws DENOPTIMException
	Generates up to a pair of new offspring by performing a crossover operation. More...
static Candidate	buildCandidateByMutation (List< Candidate > eligibleParents, Monitor mnt, GAParameters settings) throws DENOPTIMException
static Candidate	readCandidateFromFile (File srcFile, Monitor mnt, GAParameters settings) throws DENOPTIMException
static Candidate	buildCandidateFromScratch (Monitor mnt, GAParameters settings) throws DENOPTIMException
static Candidate[]	selectBasedOnFitness (List< Candidate > eligibleParents, int number, GAParameters settings)
	Selects a number of members from the given population. More...
static Vertex	selectNonScaffoldNonCapVertex (DGraph g, Randomizer randomizer)
	Chose randomly a vertex that is neither scaffold or capping group. More...
static XoverSite	performFBCC (List< Candidate > eligibleParents, Population population, int[] choiceOfParents, int choiceOfXOverSites, GAParameters settings)
	Perform fitness-based, class-compatible selection of parents that can do crossover operations. More...
static void	outputFinalResults (Population popln, GAParameters settings) throws DENOPTIMException
	Saves the final results to disk. More...
static void	getPopulationFromFile (String filename, Population population, SizeControlledSet uniqueIDsSet, String genDir, GAParameters settings) throws DENOPTIMException, IOException
	Reconstruct the molecular population from the file. More...
static void	writeUID (String outfile, HashSet< String > lstInchi, boolean append) throws DENOPTIMException
static void	setVertexCounterValue (Population population) throws DENOPTIMException
	Set the Vertex counter value according to the largest value found in the given population. More...
static DGraph	buildGraph (GAParameters settings) throws DENOPTIMException
	Graph construction starts with selecting a random core/scaffold. More...
static boolean	setupRings (Object[] res, DGraph molGraph, GAParameters settings) throws DENOPTIMException
	Evaluates the possibility of closing rings in a given graph and if any ring can be closed, it chooses one of the combinations of ring closures that involves the highest number of new rings. More...
static boolean	containsMolecule (Population mols, String molcode)
	Check if the population contains the specified InChi code. More...
static double[]	getFitnesses (Population mols)
	Get the fitness values for the list of molecules. More...
static double	getPopulationSD (Population molPopulation)
	Check if fitness values have significant standard deviation. More...
static boolean	foundForbiddenEnd (DGraph molGraph, FragmentSpaceParameters fsParams)
	Check if there are forbidden ends: free attachment points that are not suitable for capping and not allowed to stay unused. More...
static void	readUID (String infile, HashSet< String > lstInchi) throws DENOPTIMException

Static Protected Attributes
static HashMap< Integer, ArrayList< Integer > >	fragmentPool
static HashMap< Integer, ArrayList< String > >	lstFragmentClass

Static Private Member Functions
static DecimalFormat	initialiseFormatter ()
static void	appendVertexesToGraphFollowingEdges (DGraph graph, AtomicInteger vId, List< Vertex > vertexes) throws DENOPTIMException
static String	getSummaryStatistics (Population popln, GAParameters settings)

Static Private Attributes
static Locale	enUsLocale = new Locale("en", "US")
	Locale used to write reports. More...
static DecimalFormat	df = initialiseFormatter()
	Format for decimal fitness numbers that overwrites Locale to en_US. More...
static final String	NL =System.getProperty("line.separator")
static final String	FSEP = System.getProperty("file.separator")

Detailed Description

Helper methods for the genetic algorithm.

Author

Vishwesh Venkatraman

Marco Foscato

Definition at line 92 of file EAUtils.java.

Member Function Documentation

appendVertexesToGraphFollowingEdges()

static void denoptim.ga.EAUtils.appendVertexesToGraphFollowingEdges ( DGraph  graph, AtomicInteger  vId, List< Vertex >  vertexes  ) throws DENOPTIMException

staticprivate

Definition at line 1150 of file EAUtils.java.

References denoptim.graph.Edge.BondType.ANY, denoptim.ga.EAUtils.appendVertexesToGraphFollowingEdges(), denoptim.graph.APClass.ATPLUS, denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.graph.Vertex.getAP(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.fragmenter.FragmenterTools.getRCPForAP(), denoptim.graph.Vertex.isRCV, denoptim.graph.APClass.make(), denoptim.graph.APClass.RCACLASSMINUS, denoptim.graph.Vertex.setBuildingBlockType(), and denoptim.graph.Vertex.setVertexId().

Referenced by denoptim.ga.EAUtils.appendVertexesToGraphFollowingEdges(), and denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().

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buildCandidateByFragmentingMolecule()

static Candidate denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule ( IAtomContainer  mol, Monitor  mnt, GAParameters  settings, int  index  ) throws DENOPTIMException

static

Generates a candidate by fragmenting a molecule and generating the graph that reconnects all fragments to reform the original molecule.

Essentially, it converts an IAtomContainer into a DGraph and makes a Candidate out of it.

Parameters

mol	the molecule to convert.
cutRules	the cutting rules to use in the fragmentation.
mnt	the tool monitoring events for logging purposes.
settings	GA settings.
index	identifies the given IAtomContainer in a collection of systems to work on. This is used only for logging.

Exceptions

DENOPTIMException

Definition at line 928 of file EAUtils.java.

References denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.cleanup(), denoptim.logging.CounterID.CONVERTBYFRAGATTEMPTS, denoptim.graph.DGraph.embedPatternsInTemplates(), denoptim.programs.fragmenter.FragmenterParameters.embedRingsInTemplate, denoptim.logging.CounterID.FAILEDCONVERTBYFRAGATTEMPTS, denoptim.logging.CounterID.FAILEDCONVERTBYFRAGATTEMPTS_EVAL, denoptim.logging.CounterID.FAILEDCONVERTBYFRAGATTEMPTS_FRAGMENTATION, denoptim.logging.CounterID.FAILEDCONVERTBYFRAGATTEMPTS_TMPLEMBEDDING, denoptim.programs.RunTimeParameters.ParametersType.FRG_PARAMS, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.programs.fragmenter.FragmenterParameters.getCuttingRules(), denoptim.programs.fragmenter.FragmenterParameters.getEmbeddedRingsContract(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.fragmenter.FragmenterParameters.getLinearAngleLimit(), denoptim.utils.GeneralUtils.getPaddedString(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.fragmenter.FragmenterParameters.getScaffoldingPolicy(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.constants.DENOPTIMConstants.MOLDIGITS, denoptim.logging.CounterID.NEWCANDIDATEATTEMPTS, denoptim.fragmenter.FragmenterTools.prepareMolToFragmentation(), denoptim.graph.GraphPattern.RING, denoptim.graph.Candidate.setChemicalRepresentation(), denoptim.graph.DGraph.setLocalMsg(), denoptim.graph.Candidate.setName(), denoptim.graph.Candidate.setSmiles(), and denoptim.graph.Candidate.setUID().

Referenced by denoptim.ga.EvolutionaryAlgorithm.initializePopulation().

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buildCandidateByMutation()

static Candidate denoptim.ga.EAUtils.buildCandidateByMutation ( List< Candidate >  eligibleParents, Monitor  mnt, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Definition at line 630 of file EAUtils.java.

References denoptim.graph.DGraph.addCappingGroups(), denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.cleanup(), denoptim.graph.DGraph.clone(), denoptim.logging.CounterID.FAILEDMUTATTEMTS, denoptim.logging.CounterID.FAILEDMUTATTEMTS_EVAL, denoptim.logging.CounterID.FAILEDMUTATTEMTS_FORBENDS, denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM, denoptim.logging.CounterID.FAILEDMUTATTEMTS_SETUPRINGS, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpace.getCappingMap(), denoptim.fragspace.FragmentSpace.getForbiddenEndList(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.DGraph.getFreeRCVertices(), denoptim.graph.Candidate.getGeneration(), denoptim.graph.Candidate.getGraph(), denoptim.graph.DGraph.getGraphId(), denoptim.graph.DGraph.getLocalMsg(), denoptim.utils.GeneralUtils.getPaddedString(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.Candidate.getSDFFile(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.constants.DENOPTIMConstants.MOLDIGITS, denoptim.logging.CounterID.MUTATTEMPTS, denoptim.logging.CounterID.MUTPARENTSEARCH, denoptim.logging.CounterID.NEWCANDIDATEATTEMPTS, denoptim.ga.GraphOperations.performMutation(), denoptim.graph.DGraph.renumberGraphVertices(), denoptim.ga.EAUtils.selectBasedOnFitness(), denoptim.graph.Candidate.setChemicalRepresentation(), denoptim.graph.DGraph.setGraphId(), denoptim.graph.DGraph.setLocalMsg(), denoptim.graph.Candidate.setName(), denoptim.graph.Candidate.setSmiles(), denoptim.graph.Candidate.setUID(), denoptim.ga.EAUtils.setupRings(), and denoptim.io.DenoptimIO.writeGraphToSDF().

Referenced by denoptim.ga.EvolutionaryAlgorithm.makeOffspringA(), and denoptim.ga.EvolutionaryAlgorithm.makeOffspringB().

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buildCandidateByXOver() [1/2]

static Candidate denoptim.ga.EAUtils.buildCandidateByXOver ( List< Candidate >  eligibleParents, Population  population, Monitor  mnt, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Generates a new offspring by performing a crossover operation.

Parameters

eligibleParents	candidates that can be used as parents of the offspring.
population	the collection of candidates where eligible candidates are hosted.
mnt	monitoring tool used to record events during the run of the evolutionary algorithm.

Returns

a candidate chosen in a stochastic manner.

Definition at line 299 of file EAUtils.java.

References denoptim.ga.EAUtils.buildCandidateByXOver().

Referenced by denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.ga.EAUtilsTest.testAvoidRedundantXOver(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FixedStructure(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_Free(), denoptim.ga.EAUtilsTest.testBuildByXOver_Embedded_FreeBackwards(), and denoptim.ga.EAUtilsTest.testBuildByXOver_SubGraph().

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buildCandidateByXOver() [2/2]

static Candidate denoptim.ga.EAUtils.buildCandidateByXOver ( List< Candidate >  eligibleParents, Population  population, Monitor  mnt, int[]  choiceOfParents, int  choiceOfXOverSites, int  choiceOfOffstring, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Generates a new offspring by performing a crossover operation.

Parameters

eligibleParents	candidates that can be used as parents of the offspring.
population	the collection of candidates where eligible candidates are hosted.
mnt	monitoring tool used to record events during the run of the evolutionary algorithm.
choiceOfParents	a pair of indexes dictating which ones among the eligible parents we should use as parents. This avoids randomized decision making in case of test that need to be reproducible, but can be null which means "use random choice".
choiceOfXOverSites	index indicating which crossover site to use. This avoids randomized decision making in case of test that need to be reproducible, but can be null which means "use random choice".
choiceOfOffstring	index dictating which among the available two offspring (at most two, for now) is returned as result. This avoids randomized decision making in case of test that need to be reproducible, but can be null which means "use random choice".

Returns

the candidate or null if none was produced.

Exceptions

DENOPTIMException

Definition at line 333 of file EAUtils.java.

References denoptim.ga.EAUtils.buildCandidatesByXOver().

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buildCandidateFromScratch()

static Candidate denoptim.ga.EAUtils.buildCandidateFromScratch ( Monitor  mnt, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Definition at line 827 of file EAUtils.java.

References denoptim.logging.CounterID.BUILDANEWATTEMPTS, denoptim.ga.EAUtils.buildGraph(), denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.cleanup(), denoptim.logging.CounterID.FAILEDBUILDATTEMPTS, denoptim.logging.CounterID.FAILEDBUILDATTEMPTS_EVAL, denoptim.logging.CounterID.FAILEDBUILDATTEMPTS_FORBIDENDS, denoptim.logging.CounterID.FAILEDBUILDATTEMPTS_GRAPHBUILD, denoptim.logging.CounterID.FAILEDBUILDATTEMPTS_SETUPRINGS, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpace.getCappingMap(), denoptim.fragspace.FragmentSpace.getForbiddenEndList(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.DGraph.getFreeRCVertices(), denoptim.utils.GeneralUtils.getPaddedString(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.constants.DENOPTIMConstants.MOLDIGITS, denoptim.logging.CounterID.NEWCANDIDATEATTEMPTS, denoptim.graph.Candidate.setChemicalRepresentation(), denoptim.graph.DGraph.setLocalMsg(), denoptim.graph.Candidate.setName(), denoptim.graph.Candidate.setSmiles(), denoptim.graph.Candidate.setUID(), and denoptim.ga.EAUtils.setupRings().

Referenced by denoptim.ga.EvolutionaryAlgorithm.initializePopulation(), denoptim.ga.EvolutionaryAlgorithm.makeOffspringA(), and denoptim.ga.EvolutionaryAlgorithm.makeOffspringB().

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buildCandidatesByXOver() [1/2]

static List< Candidate > denoptim.ga.EAUtils.buildCandidatesByXOver ( List< Candidate >  eligibleParents, Population  population, Monitor  mnt, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Generates a pair of new offspring by performing a crossover operation.

Parameters

eligibleParents	candidates that can be used as parents of the offspring.
population	the collection of candidates where eligible candidates are hosted.
mnt	monitoring tool used to record events during the run of the evolutionary algorithm.
settings	the settings of the genetic algorithm.

Returns

a candidate chosen in a stochastic manner.

Definition at line 279 of file EAUtils.java.

References denoptim.ga.EAUtils.buildCandidatesByXOver().

Referenced by denoptim.ga.EAUtils.buildCandidateByXOver(), denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EvolutionaryAlgorithm.makeOffspringA(), and denoptim.ga.EvolutionaryAlgorithm.makeOffspringB().

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buildCandidatesByXOver() [2/2]

static List< Candidate > denoptim.ga.EAUtils.buildCandidatesByXOver ( List< Candidate >  eligibleParents, Population  population, Monitor  mnt, int[]  choiceOfParents, int  choiceOfXOverSites, int  choiceOfOffstring, GAParameters  settings, int  maxCandidatesToReturn  ) throws DENOPTIMException

staticprotected

Generates up to a pair of new offspring by performing a crossover operation.

Parameters

eligibleParents	candidates that can be used as parents of the offspring.
population	the collection of candidates where eligible candidates are hosted.
mnt	monitoring tool used to record events during the run of the evolutionary algorithm.
choiceOfParents	a pair of indexes dictating which ones among the eligible parents we should use as parents. This avoids randomized decision making in case of test that need to be reproducible, but can be null which means "use random choice".
choiceOfXOverSites	index indicating which crossover site to use. This avoids randomized decision making in case of test that need to be reproducible, but can be null which means "use random choice".
choiceOfOffstring	index dictating which among the available two offspring (at most two, for now) is returned as result. This avoids randomized decision making in case of test that need to be reproducible, but can be null which means "use random choice".
maxCandidatesToReturn	the number of offspring to return in the list. Up to 2.

Returns

the list of candidates, or an empty list.

Exceptions

DENOPTIMException

Definition at line 378 of file EAUtils.java.

References denoptim.graph.DGraph.addCappingGroups(), denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.cleanup(), denoptim.logging.CounterID.FAILEDXOVERATTEMPTS, denoptim.logging.CounterID.FAILEDXOVERATTEMPTS_EVAL, denoptim.logging.CounterID.FAILEDXOVERATTEMPTS_FINDPARENTS, denoptim.logging.CounterID.FAILEDXOVERATTEMPTS_FORBENDS, denoptim.logging.CounterID.FAILEDXOVERATTEMPTS_PERFORM, denoptim.logging.CounterID.FAILEDXOVERATTEMPTS_SETUPRINGS, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.ga.XoverSite.getA(), denoptim.ga.XoverSite.getB(), denoptim.graph.DGraph.getCandidateOwner(), denoptim.fragspace.FragmentSpace.getCappingMap(), denoptim.graph.DGraph.getChildrenTree(), denoptim.fragspace.FragmentSpace.getForbiddenEndList(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.DGraph.getFreeRCVertices(), denoptim.graph.Candidate.getGeneration(), denoptim.graph.Candidate.getGraph(), denoptim.graph.DGraph.getGraphId(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.Candidate.getName(), denoptim.graph.DGraph.getOutermostGraphOwner(), denoptim.utils.GeneralUtils.getPaddedString(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.constants.DENOPTIMConstants.MOLDIGITS, denoptim.logging.CounterID.NEWCANDIDATEATTEMPTS, denoptim.ga.EAUtils.NL, denoptim.ga.GraphOperations.performCrossover(), denoptim.ga.EAUtils.performFBCC(), denoptim.ga.XoverSite.projectToClonedGraphs(), denoptim.graph.DGraph.renumberGraphVertices(), denoptim.ga.EAUtils.selectBasedOnFitness(), denoptim.ga.EAUtils.selectNonScaffoldNonCapVertex(), denoptim.graph.Candidate.setChemicalRepresentation(), denoptim.graph.DGraph.setGraphId(), denoptim.graph.DGraph.setLocalMsg(), denoptim.graph.Candidate.setName(), denoptim.graph.Candidate.setSmiles(), denoptim.graph.Candidate.setUID(), denoptim.ga.EAUtils.setupRings(), denoptim.ga.XoverSite.toString(), denoptim.fragspace.FragmentSpace.useAPclassBasedApproach(), denoptim.io.DenoptimIO.writeGraphsToSDF(), denoptim.logging.CounterID.XOVERATTEMPTS, and denoptim.logging.CounterID.XOVERPARENTSEARCH.

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buildGraph()

static DGraph denoptim.ga.EAUtils.buildGraph ( GAParameters  settings ) throws DENOPTIMException

staticprotected

Graph construction starts with selecting a random core/scaffold.

Returns

the molecular graph representation

Exceptions

DENOPTIMException

Definition at line 1678 of file EAUtils.java.

References denoptim.graph.DGraph.addCappingGroups(), denoptim.graph.DGraph.addVertex(), denoptim.graph.DGraph.containsOrEmbedsVertex(), denoptim.ga.GraphOperations.extendGraph(), denoptim.logging.CounterID.FAILEDMUTATTEMTS, denoptim.logging.CounterID.FAILEDMUTATTEMTS_PERFORM, denoptim.graph.Template.ContractLevel.FIXED, denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.graph.Vertex.getBuildingBlockId(), denoptim.graph.rings.RingClosuresArchive.getCCFromTurningPointId(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.graph.DGraph.getMutableSites(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.rings.RingClosureParameters.getRingClosuresArchive(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.graph.DGraph.getVertexCount(), denoptim.graph.Vertex.hasFreeAP(), denoptim.logging.Monitor.increase(), denoptim.fragspace.FragmentSpace.makeRandomScaffold(), denoptim.ga.GraphOperations.performMutation(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.graph.DGraph.setCandidateClosableChains(), denoptim.graph.DGraph.setGraphId(), and denoptim.graph.DGraph.setLocalMsg().

Referenced by denoptim.ga.EAUtils.buildCandidateFromScratch(), and denoptim.ga.EAUtilsTest.testBuildGraphFromTemplateScaffold().

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chooseGenerationMethod()

static CandidateSource denoptim.ga.EAUtils.chooseGenerationMethod ( GAParameters  settings )

staticprotected

Choose one of the methods to make new Candidates.

The choice is biased by the weights of the methods as defined in the GAParameters.

Parameters

the	genetic algorithm settings

Returns

one among the possible CandidateSource excluding {@value CandidateSource::MANUAL}.

Definition at line 193 of file EAUtils.java.

References denoptim.programs.denovo.GAParameters.getConstructionWeight(), denoptim.programs.denovo.GAParameters.getCrossoverWeight(), denoptim.programs.denovo.GAParameters.getMutationWeight(), denoptim.programs.RunTimeParameters.getRandomizer(), and denoptim.ga.EAUtils.pickNewCandidateGenerationMode().

Referenced by denoptim.ga.EvolutionaryAlgorithm.makeOffspringA().

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chooseNumberOfSitesToMutate()

static int denoptim.ga.EAUtils.chooseNumberOfSitesToMutate ( double[]  multiSiteMutationProb, double  hit  )

static

Takes a decision on how many sites to mutate on a candidate.

Parameters

multiSiteMutationProb	the probability (0-1) of multi-site mutation.
hit	a random real number between 0 and 1.

Returns

an integer indicating how many mutation to perform.

Definition at line 210 of file EAUtils.java.

Referenced by denoptim.ga.GraphOperations.performMutation(), and denoptim.ga.EAUtilsTest.testChooseNumberOfSitesToMutate().

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containsMolecule()

static boolean denoptim.ga.EAUtils.containsMolecule ( Population  mols, String  molcode  )

staticprotected

Check if the population contains the specified InChi code.

Parameters

mols
molcode

Returns

true if found

Definition at line 1945 of file EAUtils.java.

createFolderForGeneration()

static void denoptim.ga.EAUtils.createFolderForGeneration ( int  genId, GAParameters  settings  )

staticprotected

Creates a folder meant to hold all the data generated during a generation.

The folder is created under the work space.

Parameters

genId

the generation's identity number

Exceptions

DENOPTIMException

Definition at line 134 of file EAUtils.java.

References denoptim.ga.EAUtils.getPathNameToGenerationFolder().

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), and denoptim.ga.EvolutionaryAlgorithm.run().

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foundForbiddenEnd()

static boolean denoptim.ga.EAUtils.foundForbiddenEnd ( DGraph  molGraph, FragmentSpaceParameters  fsParams  )

staticprotected

Check if there are forbidden ends: free attachment points that are not suitable for capping and not allowed to stay unused.

Parameters

molGraph

the Graph representation of the molecule

Returns

true if a forbidden end is found

Definition at line 2274 of file EAUtils.java.

References denoptim.fragspace.FragmentSpace.getForbiddenEndList(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getLogger(), and denoptim.graph.DGraph.getVertexList().

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getCrowdedness() [1/2]

static int denoptim.ga.EAUtils.getCrowdedness ( AttachmentPoint  ap )

static

Calculate the current crowdedness of the given attachment point.

Parameters

ap	the attachment point to consider

Returns

the integer representing how many AP rooted on the same atom that holds the given attachment point are used by non-capping group building blocks.

Definition at line 2174 of file EAUtils.java.

References denoptim.ga.EAUtils.getCrowdedness().

Referenced by denoptim.ga.GraphOperations.extendGraph(), denoptim.ga.EAUtils.getCrowdedness(), denoptim.ga.EAUtils.getCrowdingProbability(), and denoptim.ga.EAUtils.setupRings().

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getCrowdedness() [2/2]

static int denoptim.ga.EAUtils.getCrowdedness ( AttachmentPoint  ap, boolean  ignoreFreeRCVs  )

static

Calculate the current crowdedness of the given attachment point.

Parameters

ap	the attachment point to consider
ignoreFreeRCVs	use true to avoid counting unused ring-closing vertexes and actual connections.

Returns

the integer representing how many AP rooted on the same atom that holds the given attachment point are used by non-capping group building blocks. Returns zero for APs belonging to EmptyVertexs.

Definition at line 2190 of file EAUtils.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.Vertex.getAttachmentPoints(), denoptim.graph.Vertex.getGraphOwner(), denoptim.graph.AttachmentPoint.getOwner(), and denoptim.graph.DGraph.getUsedRCVertices().

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getCrowdingProbability() [1/3]

static double denoptim.ga.EAUtils.getCrowdingProbability ( AttachmentPoint  ap, GAParameters  settings  )

static

Calculated the probability of using and attachment point rooted on an atom that is holding other attachment points which have already been used.

Parameters

ap	the attachment point candidate to be used.

Returns

probability of adding a new building block on the given attachment point.

Definition at line 2129 of file EAUtils.java.

References denoptim.programs.denovo.GAParameters.getCrowdingFactorMiddleSigma(), denoptim.programs.denovo.GAParameters.getCrowdingFactorSteepSigma(), denoptim.programs.denovo.GAParameters.getCrowdingMultiplier(), denoptim.ga.EAUtils.getCrowdingProbability(), and denoptim.programs.denovo.GAParameters.getCrowdingProbabilityScheme().

Referenced by denoptim.ga.GraphOperations.extendGraph(), denoptim.ga.EAUtils.getCrowdingProbability(), denoptim.ga.EAUtils.setupRings(), and denoptim.ga.EAUtilsTest.testCrowdingProbability().

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getCrowdingProbability() [2/3]

static double denoptim.ga.EAUtils.getCrowdingProbability ( AttachmentPoint  ap, int  scheme, double  lambda, double  sigmaOne, double  sigmaTwo  )

static

Calculated the probability of using and attachment point rooted on an atom that is holding other attachment points that have already been used.

Parameters

ap	the attachment point candidate to be used.
scheme	the chosen shape of the probability function.
lambda	parameter used by scheme 0 and 1
sigmaOne	parameter used by scheme 2 (steepness)
sigmaTwo	parameter used by scheme 2 (middle point)

Returns

probability of adding a new building block on the given attachment point.

Definition at line 2232 of file EAUtils.java.

References denoptim.ga.EAUtils.getCrowdedness(), denoptim.ga.EAUtils.getCrowdingProbabilityForCrowdedness(), and denoptim.graph.AttachmentPoint.getOwner().

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getCrowdingProbability() [3/3]

static double denoptim.ga.EAUtils.getCrowdingProbability ( int  crowdedness, GAParameters  settings  )

static

Calculated the probability of using and attachment point rooted on an atom that is holding other attachment points which have already been used.

This method does not use the actual information on attachment point usage, but relies on a externally calculated values of the crowdedness. Use EAUtils#getCrowdingProbability(AttachmentPoint) to get the crowding probability for an actual attachment point. Use EAUtils#getCrowdedness(AttachmentPoint) to calculate the crowdedness for an attachment point.

Parameters

crowdedness

the level of crowdedness

Returns

probability of adding a new building block on an attachment point with the given crowdedness.

Definition at line 2154 of file EAUtils.java.

References denoptim.programs.denovo.GAParameters.getCrowdingFactorMiddleSigma(), denoptim.programs.denovo.GAParameters.getCrowdingFactorSteepSigma(), denoptim.programs.denovo.GAParameters.getCrowdingMultiplier(), denoptim.ga.EAUtils.getCrowdingProbabilityForCrowdedness(), and denoptim.programs.denovo.GAParameters.getCrowdingProbabilityScheme().

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getCrowdingProbabilityForCrowdedness()

static double denoptim.ga.EAUtils.getCrowdingProbabilityForCrowdedness ( int  crowdedness, int  scheme, double  lambda, double  sigmaOne, double  sigmaTwo  )

static

Calculated the crowding probability for a given level of crowdedness.

Parameters

crowdedness	the level of crowdedness
scheme	the chosen shape of the probability function.
lambda	parameter used by scheme 0 and 1
sigmaOne	parameter used by scheme 2 (steepness)
sigmaTwo	parameter used by scheme 2 (middle point)

Returns

the crowding probability.

Definition at line 2257 of file EAUtils.java.

References denoptim.ga.EAUtils.getProbability().

Referenced by denoptim.gui.GAParametersForm.createCrowdProbDataset(), and denoptim.ga.EAUtils.getCrowdingProbability().

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getFitnesses()

static double[] denoptim.ga.EAUtils.getFitnesses ( Population  mols )

staticprotected

Get the fitness values for the list of molecules.

Parameters

mols

Returns

array of fitness values

Definition at line 1968 of file EAUtils.java.

Referenced by denoptim.ga.EAUtils.getPopulationSD(), and denoptim.ga.EAUtils.getSummaryStatistics().

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getGrowthByLevelProbability()

static double denoptim.ga.EAUtils.getGrowthByLevelProbability ( int  level, GAParameters  settings  )

static

Calculates the probability of adding a fragment to the given level.

Used the settings defined by the GAParameters class.

Parameters

level

level of the graph at which fragment is to be added

Returns

probability of adding a new fragment at this level.

Definition at line 2106 of file EAUtils.java.

References denoptim.programs.denovo.GAParameters.getGrowthFactorMiddleSigma(), denoptim.programs.denovo.GAParameters.getGrowthFactorSteepSigma(), denoptim.programs.denovo.GAParameters.getGrowthMultiplier(), denoptim.ga.EAUtils.getGrowthProbabilityAtLevel(), denoptim.programs.denovo.GAParameters.getGrowthProbabilityScheme(), and denoptim.programs.denovo.GAParameters.useLevelBasedProb.

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

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getGrowthProbabilityAtLevel()

static double denoptim.ga.EAUtils.getGrowthProbabilityAtLevel ( int  level, int  scheme, double  lambda, double  sigmaOne, double  sigmaTwo  )

static

Calculates the probability of adding a fragment to the given level.

This will require a coin toss with the calculated probability. If a newly drawn random number is less than this value, a new fragment may be added.

Parameters

level	level of the graph at which fragment is to be added
scheme	the chosen scheme.
lambda	parameter used by scheme 0 and 1.
sigmaOne	parameter used by scheme 2 (steepness).
sigmaTwo	parameter used by scheme 2 (middle point).

Returns

probability of adding a new fragment at this level.

Definition at line 2009 of file EAUtils.java.

References denoptim.ga.EAUtils.getProbability().

Referenced by denoptim.gui.GAParametersForm.createLvlProbDataset(), and denoptim.ga.EAUtils.getGrowthByLevelProbability().

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getMolSizeProbability() [1/2]

static double denoptim.ga.EAUtils.getMolSizeProbability ( DGraph  graph, GAParameters  settings  )

static

Calculated the probability of extending a graph based on the current size of the molecular representation contained in the graph and the given parameters.

Parameters

graph	the current graph for which to calculate the probability of extension.
scheme	the chosen shape of the probability function.
lambda	parameter used by scheme 0 and 1
sigmaOne	parameter used by scheme 2 (steepness)
sigmaTwo	parameter used by scheme 2 (middle point)

Returns

the crowding probability.

Definition at line 2029 of file EAUtils.java.

References denoptim.programs.denovo.GAParameters.getMolGrowthFactorMiddleSigma(), denoptim.programs.denovo.GAParameters.getMolGrowthFactorSteepSigma(), denoptim.programs.denovo.GAParameters.getMolGrowthMultiplier(), denoptim.programs.denovo.GAParameters.getMolGrowthProbabilityScheme(), denoptim.ga.EAUtils.getMolSizeProbability(), and denoptim.programs.denovo.GAParameters.useMolSizeBasedProb.

Referenced by denoptim.ga.GraphOperations.extendGraph(), and denoptim.ga.EAUtils.getMolSizeProbability().

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getMolSizeProbability() [2/2]

static double denoptim.ga.EAUtils.getMolSizeProbability ( DGraph  graph, int  scheme, double  lambda, double  sigmaOne, double  sigmaTwo  )

static

Calculated the probability of extending a graph based on the current size of the molecular representation contained in the graph and the given parameters.

Parameters

graph	the current graph for which to calculate the probability of extension.
scheme	the chosen shape of the probability function.
lambda	parameter used by scheme 0 and 1
sigmaOne	parameter used by scheme 2 (steepness)
sigmaTwo	parameter used by scheme 2 (middle point)

Returns

the crowding probability.

Definition at line 2055 of file EAUtils.java.

References denoptim.graph.DGraph.getHeavyAtomsCount(), and denoptim.ga.EAUtils.getProbability().

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getPathNameToFinalPopulationDetailsFile()

static String denoptim.ga.EAUtils.getPathNameToFinalPopulationDetailsFile ( GAParameters  settings )

static

Definition at line 1494 of file EAUtils.java.

References denoptim.ga.EAUtils.FSEP, and denoptim.programs.denovo.GAParameters.getDataDirectory().

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

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getPathNameToFinalPopulationFolder()

static String denoptim.ga.EAUtils.getPathNameToFinalPopulationFolder ( GAParameters  settings )

static

Definition at line 1485 of file EAUtils.java.

References denoptim.ga.EAUtils.FSEP, and denoptim.programs.denovo.GAParameters.getDataDirectory().

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

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getPathNameToGenerationDetailsFile()

static String denoptim.ga.EAUtils.getPathNameToGenerationDetailsFile ( int  genID, GAParameters  settings  )

static

Definition at line 1465 of file EAUtils.java.

References denoptim.ga.EAUtils.FSEP, denoptim.constants.DENOPTIMConstants.GAGENDIRNAMEROOT, denoptim.programs.denovo.GAParameters.getDataDirectory(), denoptim.programs.denovo.GAParameters.getNumberOfGenerations(), and denoptim.utils.GeneralUtils.getPaddedString().

Referenced by denoptim.ga.EvolutionaryAlgorithm.run(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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getPathNameToGenerationFolder()

static String denoptim.ga.EAUtils.getPathNameToGenerationFolder ( int  genID, GAParameters  settings  )

static

Definition at line 1449 of file EAUtils.java.

References denoptim.ga.EAUtils.FSEP, denoptim.constants.DENOPTIMConstants.GAGENDIRNAMEROOT, denoptim.programs.denovo.GAParameters.getDataDirectory(), denoptim.programs.denovo.GAParameters.getNumberOfGenerations(), and denoptim.utils.GeneralUtils.getPaddedString().

Referenced by denoptim.ga.EAUtils.createFolderForGeneration(), denoptim.ga.EvolutionaryAlgorithm.evolvePopulation(), denoptim.ga.EAUtils.importInitialPopulation(), denoptim.ga.EvolutionaryAlgorithm.processInitialPopCandidate(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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getPopulationFromFile()

static void denoptim.ga.EAUtils.getPopulationFromFile ( String  filename, Population  population, SizeControlledSet  uniqueIDsSet, String  genDir, GAParameters  settings  ) throws DENOPTIMException, IOException

staticprotected

Reconstruct the molecular population from the file.

Parameters

filename	the pathname to read in.
population	the collection of population members.
uniqueIDsSet	collection of unique identifiers.

Exceptions

DENOPTIMException
IOException

Definition at line 1573 of file EAUtils.java.

References denoptim.constants.DENOPTIMConstants.FITFILENAMEEXTOUT, denoptim.utils.GeneralUtils.getPaddedString(), denoptim.utils.GraphUtils.getUniqueGraphIndex(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.io.DenoptimIO.readCandidates(), denoptim.ga.EAUtils.setVertexCounterValue(), and denoptim.io.DenoptimIO.writeCandidateToFile().

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

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getPopulationSD()

static double denoptim.ga.EAUtils.getPopulationSD ( Population  molPopulation )

staticprotected

Check if fitness values have significant standard deviation.

Parameters

molPopulation

Returns

true if population standard deviation of fitness values exceeds 0.0001

Definition at line 1989 of file EAUtils.java.

References denoptim.ga.EAUtils.getFitnesses(), and denoptim.utils.StatUtils.stddev().

Referenced by denoptim.ga.EvolutionaryAlgorithm.run().

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getProbability()

static double denoptim.ga.EAUtils.getProbability ( double  value, int  scheme, double  lambda, double  sigmaOne, double  sigmaTwo  )

static

Calculated a probability given parameters defining the shape of the probability function and a single input value.

Parameters

value	the value x for which we calculate f(x).
scheme	the chosen shape of the probability function.
lambda	parameter used by scheme 0 and 1
sigmaOne	parameter used by scheme 2 (steepness)
sigmaTwo	parameter used by scheme 2 (middle point)

Returns

the probability.

Definition at line 2074 of file EAUtils.java.

Referenced by denoptim.gui.GAParametersForm.createMolSizeProbDataset(), denoptim.ga.EAUtils.getCrowdingProbabilityForCrowdedness(), denoptim.ga.EAUtils.getGrowthProbabilityAtLevel(), and denoptim.ga.EAUtils.getMolSizeProbability().

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getSummaryStatistics()

static String denoptim.ga.EAUtils.getSummaryStatistics ( Population  popln, GAParameters  settings  )

staticprivate

Definition at line 1285 of file EAUtils.java.

References denoptim.ga.EAUtils.df, denoptim.ga.EAUtils.getFitnesses(), denoptim.programs.denovo.GAParameters.getPrecisionLevel(), denoptim.utils.StatUtils.max(), denoptim.utils.StatUtils.mean(), denoptim.utils.StatUtils.median(), denoptim.utils.StatUtils.min(), denoptim.ga.EAUtils.NL, denoptim.utils.StatUtils.skewness(), and denoptim.utils.StatUtils.stddev().

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

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importInitialPopulation()

static Population denoptim.ga.EAUtils.importInitialPopulation ( SizeControlledSet  uniqueIDsSet, GAParameters  settings  ) throws DENOPTIMException, IOException

staticprotected

Reads unique identifiers and initial population file according to the GAParameters.

Exceptions

IOException

Definition at line 148 of file EAUtils.java.

References denoptim.ga.EAUtils.getPathNameToGenerationFolder(), denoptim.ga.EAUtils.getPopulationFromFile(), and denoptim.ga.EAUtils.readUID().

Referenced by denoptim.ga.EvolutionaryAlgorithm.run().

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initialiseFormatter()

static DecimalFormat denoptim.ga.EAUtils.initialiseFormatter ( )

staticprivate

Definition at line 106 of file EAUtils.java.

References denoptim.ga.EAUtils.df, and denoptim.ga.EAUtils.enUsLocale.

makeGraphFromFragmentationOfMol() [1/2]

static DGraph denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol ( IAtomContainer  mol, List< CuttingRule >  cuttingRules, Logger  logger, ScaffoldingPolicy  scaffoldingPolicy  ) throws DENOPTIMException

static

Converts a molecule into a DGraph by fragmentation and re-assembling of the fragments.

Parameters

mol	the molecule to convert
cuttingRules	the cutting rules defining how to do fragmentation.
logger	tool managing log.
scaffoldingPolicy	the policy for deciding which vertex should be given the role of scaffold.

Returns

the graph.

Exceptions

DENOPTIMException

Definition at line 1028 of file EAUtils.java.

References denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol().

Referenced by denoptim.gui.GUIGraphHandler.appendGraphsFromConvertingMolecule(), denoptim.ga.EAUtils.buildCandidateByFragmentingMolecule(), denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_linearities(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_ScaffoldingPolicy(), denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_Symmetry(), and denoptim.ga.EAUtilsTest.testMakeGraphFromFragmentationOfMol_symmetry().

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makeGraphFromFragmentationOfMol() [2/2]

static DGraph denoptim.ga.EAUtils.makeGraphFromFragmentationOfMol ( IAtomContainer  mol, List< CuttingRule >  cuttingRules, Logger  logger, ScaffoldingPolicy  scaffoldingPolicy, double  linearAngleLimit  ) throws DENOPTIMException

static

Converts a molecule into a DGraph by fragmentation and re-assembling of the fragments.

Parameters

mol	the molecule to convert
cuttingRules	the cutting rules defining how to do fragmentation.
logger	tool managing log.
scaffoldingPolicy	the policy for deciding which vertex should be given the role of scaffold.
linearAngleLimit	the max bond angle before we start considering the angle linear and add a linearity-breaking dummy atom.

Returns

the graph.

Exceptions

DENOPTIMException

Definition at line 1053 of file EAUtils.java.

References denoptim.utils.DummyAtomHandler.addDummiesOnLinearities(), denoptim.graph.DGraph.addVertex(), denoptim.ga.EAUtils.appendVertexesToGraphFollowingEdges(), denoptim.graph.DGraph.detectSymVertexSets(), denoptim.fragmenter.FragmenterTools.fragmentation(), denoptim.graph.Vertex.getHeavyAtomsCount(), denoptim.graph.Vertex.getIAtomContainer(), denoptim.utils.MoleculeUtils.getSymbolOrLabel(), denoptim.graph.Vertex.BBType.SCAFFOLD, denoptim.graph.Vertex.setBuildingBlockType(), denoptim.graph.Vertex.setVertexId(), and denoptim.graph.Fragment.updateAPs().

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outputFinalResults()

static void denoptim.ga.EAUtils.outputFinalResults ( Population  popln, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Saves the final results to disk.

If the files for each candidate have been saved on disk along the way, then it copies them from their location into the folder for final results, which is defined based on the GA settings.

Parameters

popln	the final list of best molecules
settings	the GS settings containing defaults and parameters given by the user.

Definition at line 1515 of file EAUtils.java.

References denoptim.programs.RunTimeParameters.ParametersType.FIT_PARAMS, denoptim.constants.DENOPTIMConstants.FITFILENAMEEXTOUT, denoptim.graph.Candidate.getImageFile(), denoptim.graph.Candidate.getName(), denoptim.ga.EAUtils.getPathNameToFinalPopulationDetailsFile(), denoptim.ga.EAUtils.getPathNameToFinalPopulationFolder(), denoptim.graph.Candidate.getSDFFile(), denoptim.ga.EAUtils.outputPopulationDetails(), denoptim.graph.Candidate.setSDFFile(), and denoptim.io.DenoptimIO.writeCandidateToFile().

Referenced by denoptim.ga.EvolutionaryAlgorithm.run().

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outputPopulationDetails()

static void denoptim.ga.EAUtils.outputPopulationDetails ( Population  population, String  filename, GAParameters  settings, boolean  printpathNames  ) throws DENOPTIMException

static

Write out summary for the current GA population.

Parameters

population
filename	the pathname of the file where we write the details of the population. If required by the GAParameters, we use this also to define a pathname where to write all the members of the population.

Exceptions

DENOPTIMException

Definition at line 1226 of file EAUtils.java.

References denoptim.ga.EAUtils.df, denoptim.constants.DENOPTIMConstants.GAGENSUMMARYHEADER, denoptim.graph.Candidate.getFitness(), denoptim.graph.Candidate.getGraph(), denoptim.graph.DGraph.getGraphId(), denoptim.graph.Candidate.getName(), denoptim.graph.Candidate.getSDFFile(), denoptim.ga.EAUtils.getSummaryStatistics(), denoptim.graph.Candidate.getUID(), denoptim.ga.EAUtils.NL, denoptim.io.DenoptimIO.writeCandidatesToFile(), and denoptim.io.DenoptimIO.writeData().

Referenced by denoptim.ga.EAUtils.outputFinalResults(), denoptim.ga.EvolutionaryAlgorithm.run(), and denoptim.io.DenoptimIOTest.testReadGenerationFromSummary().

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performFBCC()

static XoverSite denoptim.ga.EAUtils.performFBCC ( List< Candidate >  eligibleParents, Population  population, int[]  choiceOfParents, int  choiceOfXOverSites, GAParameters  settings  )

staticprotected

Perform fitness-based, class-compatible selection of parents that can do crossover operations.

Parameters

eligibleParents	list of candidates among which to choose.
population	the dynamic population containing the eligible parents.
choiceOfParents	the integers dictating the selection of parents. Use this only to ensure reproducibility in tests, otherwise use null
choiceOfXOverSites	the integers dictating the selection of crossover sites. Use this only to ensure reproducibility in tests, otherwise use negative

Returns

returns the definition of the crossover in terms of subgraphs to swap.

Definition at line 1399 of file EAUtils.java.

References denoptim.programs.RunTimeParameters.containsParameters(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.programs.RunTimeParameters.getRandomizer(), denoptim.ga.Population.getXoverPartners(), denoptim.ga.Population.getXoverSites(), denoptim.utils.Randomizer.randomlyChooseOne(), and denoptim.ga.EAUtils.selectBasedOnFitness().

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

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pickNewCandidateGenerationMode()

static CandidateSource denoptim.ga.EAUtils.pickNewCandidateGenerationMode ( double  xoverWeight, double  mutWeight, double  newWeight, Randomizer  randomizer  )

static

Takes a decision on which CandidateSource method to use for generating a new Candidate.

The choice is made according to the weights given as arguments, and shooting a random number over a weighted score range.

Parameters

xoverWeight	weight of crossover between existing population members.
mutWeight	weight of mutation of existing population members.
newWeight	weight of construction from scratch.

Returns

one among the possible CandidateSource excluding {@value CandidateSource::MANUAL}.

Definition at line 249 of file EAUtils.java.

References denoptim.ga.EAUtils.CandidateSource.CONSTRUCTION, denoptim.ga.EAUtils.CandidateSource.CROSSOVER, denoptim.ga.EAUtils.CandidateSource.MUTATION, and denoptim.utils.Randomizer.nextDouble().

Referenced by denoptim.ga.EAUtils.chooseGenerationMethod(), denoptim.ga.EvolutionaryAlgorithm.makeOffspringB(), denoptim.ga.EAUtilsTest.testCandidateGenerationMethod(), and denoptim.ga.EAUtilsTest.testCandidateGenerationMethodReproducibility().

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readCandidateFromFile()

static Candidate denoptim.ga.EAUtils.readCandidateFromFile ( File  srcFile, Monitor  mnt, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Definition at line 754 of file EAUtils.java.

References denoptim.graph.DGraph.checkConsistency(), denoptim.graph.DGraph.cleanup(), denoptim.logging.CounterID.FAILEDMANUALADDATTEMPTS, denoptim.logging.CounterID.FAILEDMANUALADDATTEMPTS_EVAL, denoptim.graph.Candidate.getName(), denoptim.utils.GeneralUtils.getPaddedString(), denoptim.utils.GraphUtils.getUniqueMoleculeIndex(), denoptim.logging.CounterID.MANUALADDATTEMPTS, denoptim.constants.DENOPTIMConstants.MOLDIGITS, denoptim.logging.CounterID.NEWCANDIDATEATTEMPTS, denoptim.io.DenoptimIO.readDENOPTIMGraphsFromFile(), denoptim.graph.Candidate.setChemicalRepresentation(), denoptim.graph.DGraph.setLocalMsg(), denoptim.graph.Candidate.setName(), denoptim.graph.Candidate.setSmiles(), and denoptim.graph.Candidate.setUID().

Referenced by denoptim.ga.EvolutionaryAlgorithm.evolvePopulation().

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readUID()

static void denoptim.ga.EAUtils.readUID ( String  infile, HashSet< String >  lstInchi  ) throws DENOPTIMException

staticprotected

Definition at line 2307 of file EAUtils.java.

References denoptim.io.DenoptimIO.readList().

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

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searchForApSuitableToRingClosure()

static AttachmentPoint denoptim.ga.EAUtils.searchForApSuitableToRingClosure ( AttachmentPoint  apA, SymmetricAPs  symAPsA, GAParameters  settings  )

static

Definition at line 2318 of file EAUtils.java.

selectBasedOnFitness()

static Candidate[] denoptim.ga.EAUtils.selectBasedOnFitness ( List< Candidate >  eligibleParents, int  number, GAParameters  settings  )

staticprotected

Selects a number of members from the given population.

The selection method is what specified by the configuration of the genetic algorithm (GAParameters).

Parameters

eligibleParents	the list of candidates to chose from.
number	how many candidate to pick.

Returns

indexes of the selected members of the given population.

Definition at line 1342 of file EAUtils.java.

References denoptim.programs.denovo.GAParameters.getSelectionStrategyType(), denoptim.ga.SelectionHelper.performRandomSelection(), denoptim.ga.SelectionHelper.performRWS(), denoptim.ga.SelectionHelper.performSUS(), and denoptim.ga.SelectionHelper.performTournamentSelection().

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidatesByXOver(), and denoptim.ga.EAUtils.performFBCC().

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selectNonScaffoldNonCapVertex()

static Vertex denoptim.ga.EAUtils.selectNonScaffoldNonCapVertex ( DGraph  g, Randomizer  randomizer  )

staticprotected

Chose randomly a vertex that is neither scaffold or capping group.

Definition at line 1371 of file EAUtils.java.

References denoptim.graph.Vertex.BBType.CAP, denoptim.graph.DGraph.getVertexList(), denoptim.utils.Randomizer.randomlyChooseOne(), and denoptim.graph.Vertex.BBType.SCAFFOLD.

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), and denoptim.ga.EAUtilsTest.testSelectNonScaffoldNonCapVertex().

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setupRings()

static boolean denoptim.ga.EAUtils.setupRings ( Object[]  res, DGraph  molGraph, GAParameters  settings  ) throws DENOPTIMException

staticprotected

Evaluates the possibility of closing rings in a given graph and if any ring can be closed, it chooses one of the combinations of ring closures that involves the highest number of new rings.

Parameters

res	an object array containing the inchi code, the smiles string and the 2D representation of the molecule. This object can be null if inchi/smiles/2D conversion fails.
molGraph	the DENOPTIMGraph on which rings are to be identified

Returns

true unless no ring can be set up even if required

Definition at line 1773 of file EAUtils.java.

References denoptim.graph.rings.RingClosureParameters.allowRingClosures(), denoptim.graph.rings.RingClosureParameters.buildChelatesMode, denoptim.graph.rings.CyclicGraphHandler.checkChelatesGraph(), denoptim.molecularmodeling.ThreeDimTreeBuilder.convertGraphTo3DAtomContainer(), denoptim.utils.RotationalSpaceUtils.defineRotatableBonds(), denoptim.programs.RunTimeParameters.ParametersType.FS_PARAMS, denoptim.ga.EAUtils.getCrowdedness(), denoptim.ga.EAUtils.getCrowdingProbability(), denoptim.fragspace.FragmentSpaceParameters.getFragmentSpace(), denoptim.utils.MoleculeUtils.getInChIKeyForMolecule(), denoptim.graph.rings.RingClosureParameters.getMaxRingClosures(), denoptim.programs.RunTimeParameters.getParameters(), denoptim.graph.rings.CyclicGraphHandler.getPossibleCombinationOfRings(), denoptim.graph.rings.CyclicGraphHandler.getRandomCombinationOfRings(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), denoptim.programs.RunTimeParameters.ParametersType.RC_PARAMS, denoptim.molecularmodeling.ThreeDimTreeBuilder.setAlignBBsIn3D(), and denoptim.fragspace.FragmentSpace.useAPclassBasedApproach().

Referenced by denoptim.ga.EAUtils.buildCandidateByMutation(), denoptim.ga.EAUtils.buildCandidateFromScratch(), and denoptim.ga.EAUtils.buildCandidatesByXOver().

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setVertexCounterValue()

static void denoptim.ga.EAUtils.setVertexCounterValue ( Population  population ) throws DENOPTIMException

staticprotected

Set the Vertex counter value according to the largest value found in the given population.

Parameters

population

the collection of candidates to analyse.

Exceptions

DENOPTIMException

Definition at line 1657 of file EAUtils.java.

References denoptim.utils.GraphUtils.ensureVertexIDConsistency(), and denoptim.graph.DGraph.getMaxVertexId().

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

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writeUID()

static void denoptim.ga.EAUtils.writeUID ( String  outfile, HashSet< String >  lstInchi, boolean  append  ) throws DENOPTIMException

staticprotected

Definition at line 1624 of file EAUtils.java.

References denoptim.ga.EAUtils.NL, and denoptim.io.DenoptimIO.writeData().

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Member Data Documentation

df

DecimalFormat denoptim.ga.EAUtils.df = initialiseFormatter()

staticprivate

Format for decimal fitness numbers that overwrites Locale to en_US.

Definition at line 105 of file EAUtils.java.

Referenced by denoptim.ga.EAUtils.getSummaryStatistics(), denoptim.ga.EAUtils.initialiseFormatter(), and denoptim.ga.EAUtils.outputPopulationDetails().

enUsLocale

Locale denoptim.ga.EAUtils.enUsLocale = new Locale("en", "US")

staticprivate

Locale used to write reports.

Definition at line 100 of file EAUtils.java.

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

fragmentPool

HashMap<Integer, ArrayList<Integer> > denoptim.ga.EAUtils.fragmentPool

staticprotected

Definition at line 95 of file EAUtils.java.

FSEP

final String denoptim.ga.EAUtils.FSEP = System.getProperty("file.separator")

staticprivate

Definition at line 124 of file EAUtils.java.

Referenced by denoptim.ga.EAUtils.getPathNameToFinalPopulationDetailsFile(), denoptim.ga.EAUtils.getPathNameToFinalPopulationFolder(), denoptim.ga.EAUtils.getPathNameToGenerationDetailsFile(), and denoptim.ga.EAUtils.getPathNameToGenerationFolder().

lstFragmentClass

HashMap<Integer, ArrayList<String> > denoptim.ga.EAUtils.lstFragmentClass

staticprotected

Definition at line 114 of file EAUtils.java.

NL

final String denoptim.ga.EAUtils.NL =System.getProperty("line.separator")

staticprivate

Definition at line 123 of file EAUtils.java.

Referenced by denoptim.ga.EAUtils.buildCandidatesByXOver(), denoptim.ga.EAUtils.getSummaryStatistics(), denoptim.ga.EAUtils.outputPopulationDetails(), and denoptim.ga.EAUtils.writeUID().

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

• /github/workspace/src/main/java/denoptim/ga/EAUtils.java