Task that analyzes an isomorphic family of fragments to identify the most representative fragment (i.e., the champion). More...

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Public Member Functions
	ConformerExtractorTask (List< Vertex > isomorphicFamily, FragmenterParameters settings) throws SecurityException, IOException
	Constructs a task that will analyze the given isomorphic family. More...

	ConformerExtractorTask (Vertex oldChampions, FragmenterParameters settings) throws SecurityException, IOException
	Constructs a task that will analyze the isomorphic family of the given fragment. More...

String	getLogFilePathname ()

Object	call () throws Exception

String	getResultFile ()

Public Member Functions inherited from denoptim.task.Task
	Task (final int id)

int	getId ()

void	setVerbosity (int verbosity)
	Set the verbosity: i.e., amount of log printed by this class. More...

void	setWorkSpace (File workDir)
	Sets the pathname of the work space, i.e., the location where the task is supposed to use move to or to threat as the result of "pwd" at runtime. More...

boolean	isCompleted ()

boolean	foundException ()

Throwable	getException ()

String	getErrorMessage ()

void	stopTask ()
	Stop the task if not already completed. More...

String	toString ()
	Returns a string identifying this task by its ID and reporting whether an exception has been thrown and if the tasks is completed. More...

void	setNotify (boolean notify)

Static Public Member Functions
static List< ClusterableFragment >	extractClusterableFragments (Iterator< IAtomContainer > reader, String isomorphicFamilyId, Logger logger)
	Analyzes all the entries provided by the iterator and extracts those that pertain the specified isomorphic family. More...

static boolean	populateListOfClusterizableFragments (List< ClusterableFragment > sample, Fragment frag, Logger logger, String fragId)
	Tries to add a fragment into a sample of isomorphic fragments. More...

Protected Attributes
String	results = null
	The data structure holding the results of this task. More...

FragmenterParameters	settings
	Settings for the calculation of the fitness. More...

Protected Attributes inherited from denoptim.task.Task
boolean	notifyGlobalTaskManager = false
	Flag controlling whether this task is expected to notify the static task manager. More...

boolean	completed = false
	Flag about completion. More...

boolean	hasException = false
	Flag about exception. More...

String	errMsg = ""
	Error message produced by any subtask. More...

Throwable	thrownExc
	Exception thrown. More...

int	id
	A user-assigned id for this task. More...

ProcessHandler	processHandler
	Executor for external bash script. More...

File	workDir
	The file system location where we want to be placed when doing the work. More...

int	verbosity = 0
	Verbosity level. More...

final String	SEP = System.getProperty("file.separator")
	System-dependent file separator. More...

final String	NL = System.getProperty("line.separator")
	System-dependent line separator (newline) More...

Static Package Functions
static String	getClusterPathname (FragmenterParameters settings, String isomorphicFamilyId, int i)
	Builds the pathname for the file where we save the members of a given cluster. More...

static String	getClusterCentroidsPathname (FragmenterParameters settings, String isomorphicFamilyId)
	Builds the pathname for the file where we save all the centroids of clusters. More...

static String	getChosenFragPathname (FragmenterParameters settings, String isomorphicFamilyId)
	Builds the pathname for the file where we save all the fragments that we found to be closest to each cluster's centroid. More...

Private Member Functions
List< ClusterableFragment >	collectClusterableFragmentsFromFile () throws DENOPTIMException
	Collects the clusterable fragments from the disk. More...

Private Attributes
String	isomorphicFamilyId = null
	Identifier of the isomorphic family this task deals with. More...

File	isoFamMembersFile
	File collecting (among others) the sampled members of the isomorphic family. More...

List< ClusterableFragment >	sample
	List of fragments defining an isomorphic family to analyse. More...

Logger	logger = null
	Logger for this task. More...

String	logFilePathname = "unset"
	Pathname to thread-specific log. More...

Additional Inherited Members
Public Attributes inherited from denoptim.task.Task
Object	lock = new Object()
	Lock for addressing synchronization issues. More...

Detailed Description

Task that analyzes an isomorphic family of fragments to identify the most representative fragment (i.e., the champion).

The champion is extracted as the result of this task so that it is made available for further usage.

Definition at line 57 of file ConformerExtractorTask.java.

Constructor & Destructor Documentation

◆ ConformerExtractorTask() [1/2]

denoptim.fragmenter.ConformerExtractorTask.ConformerExtractorTask	(	List< Vertex >	isomorphicFamily,
		FragmenterParameters	settings
	)		throws SecurityException, IOException

Constructs a task that will analyze the given isomorphic family.

Parameters

isomorphicFamily	the fragments belonging to the isomorphic family to analyze. We do check for isomorphism and keep only the fragments that have an isomorphism with the first fragment in this list.
settings	parameters controlling the job.

Exceptions

SecurityException
IOException

Definition at line 106 of file ConformerExtractorTask.java.

References denoptim.programs.RunTimeParameters.getLogger(), denoptim.utils.TaskUtils.getUniqueTaskIndex(), denoptim.fragmenter.ConformerExtractorTask.logger, denoptim.fragmenter.ConformerExtractorTask.populateListOfClusterizableFragments(), denoptim.fragmenter.ConformerExtractorTask.sample, and denoptim.fragmenter.ConformerExtractorTask.settings.

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◆ ConformerExtractorTask() [2/2]

denoptim.fragmenter.ConformerExtractorTask.ConformerExtractorTask	(	Vertex	oldChampions,
		FragmenterParameters	settings
	)		throws SecurityException, IOException

Constructs a task that will analyze the isomorphic family of the given fragment.

We expect to find the rest of its family in filenames conventionally names according to FragmenterParameters#getMWSlotFileNameAllFrags(String).

Parameters

oldChampions	one of the fragments belonging to the isomorphic family to analyze.
settings	parameters controlling the job.

Exceptions

SecurityException
IOException

Definition at line 143 of file ConformerExtractorTask.java.

References denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.fragmenter.FragmenterParameters.getMWSlotFileNameAllFrags(), denoptim.fragmenter.FragmenterTools.getMWSlotIdentifier(), denoptim.programs.fragmenter.FragmenterParameters.getMWSlotSize(), denoptim.utils.TaskUtils.getUniqueTaskIndex(), denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.fragmenter.ConformerExtractorTask.isoFamMembersFile, denoptim.constants.DENOPTIMConstants.ISOMORPHICFAMILYID, denoptim.fragmenter.ConformerExtractorTask.isomorphicFamilyId, denoptim.fragmenter.ConformerExtractorTask.logFilePathname, denoptim.fragmenter.ConformerExtractorTask.logger, and denoptim.fragmenter.ConformerExtractorTask.settings.

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Member Function Documentation

◆ call()

Object denoptim.fragmenter.ConformerExtractorTask.call ( ) throws Exception

Definition at line 202 of file ConformerExtractorTask.java.

Referenced by denoptim.programs.fragmenter.Fragmenter.runProgram().

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◆ collectClusterableFragmentsFromFile()

List< ClusterableFragment > denoptim.fragmenter.ConformerExtractorTask.collectClusterableFragmentsFromFile ( ) throws DENOPTIMException

private

Collects the clusterable fragments from the disk.

These fragments are fragment with a list having a consistent ordering of the atoms/APs, so that such order can be used to calculate RMSD between fragments.

Returns

Exceptions

DENOPTIMException

Definition at line 271 of file ConformerExtractorTask.java.

References denoptim.fragmenter.ConformerExtractorTask.extractClusterableFragments(), denoptim.fragmenter.ConformerExtractorTask.isoFamMembersFile, denoptim.fragmenter.ConformerExtractorTask.isomorphicFamilyId, and denoptim.fragmenter.ConformerExtractorTask.logger.

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

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◆ extractClusterableFragments()

static List< ClusterableFragment > denoptim.fragmenter.ConformerExtractorTask.extractClusterableFragments	(	Iterator< IAtomContainer >	reader,
		String	isomorphicFamilyId,
		Logger	logger
	)

static

Analyzes all the entries provided by the iterator and extracts those that pertain the specified isomorphic family.

Parameters

reader	the iterator providing the input.
isomorphicFamilyId	the identifier of the isomorphic family to work with.
logger	task dedicated logger.

Returns: a list of fragments where each fragment has a consistent ordering of its atoms/APs that reflects the isomorphic mapping and allows to compare the fragments geometrically.

Definition at line 318 of file ConformerExtractorTask.java.

References denoptim.constants.DENOPTIMConstants.ISOMORPHICFAMILYID, denoptim.fragmenter.ConformerExtractorTask.isomorphicFamilyId, denoptim.fragmenter.ConformerExtractorTask.logger, denoptim.programs.fragmenter.FragmenterParameters.MAXISOMORPHICSAMPLESIZE, denoptim.fragmenter.ConformerExtractorTask.populateListOfClusterizableFragments(), denoptim.fragmenter.ConformerExtractorTask.sample, and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.fragmenter.ConformerExtractorTask.collectClusterableFragmentsFromFile(), and denoptim.fragmenter.ConformerExtractorTaskTest.testExtractClusterableFragments().

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◆ getChosenFragPathname()

static String denoptim.fragmenter.ConformerExtractorTask.getChosenFragPathname	(	FragmenterParameters	settings,
		String	isomorphicFamilyId
	)

staticpackage

Builds the pathname for the file where we save all the fragments that we found to be closest to each cluster's centroid.

Parameters

settings settings we work with.

Returns: the pathname

Definition at line 482 of file ConformerExtractorTask.java.

References denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.fragmenter.ConformerExtractorTask.isomorphicFamilyId, and denoptim.fragmenter.ConformerExtractorTask.settings.

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

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◆ getClusterCentroidsPathname()

static String denoptim.fragmenter.ConformerExtractorTask.getClusterCentroidsPathname	(	FragmenterParameters	settings,
		String	isomorphicFamilyId
	)

staticpackage

Builds the pathname for the file where we save all the centroids of clusters.

Parameters

settings settings we work with.

Returns: the pathname

Definition at line 467 of file ConformerExtractorTask.java.

References denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.fragmenter.ConformerExtractorTask.isomorphicFamilyId, and denoptim.fragmenter.ConformerExtractorTask.settings.

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

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◆ getClusterPathname()

static String denoptim.fragmenter.ConformerExtractorTask.getClusterPathname	(	FragmenterParameters	settings,
		String	isomorphicFamilyId,
		int	i
	)

staticpackage

Builds the pathname for the file where we save the members of a given cluster.

Parameters

settings	settings we work with.
i	the index of the cluster

Returns: the pathname

Definition at line 452 of file ConformerExtractorTask.java.

References denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.fragmenter.ConformerExtractorTask.isomorphicFamilyId, and denoptim.fragmenter.ConformerExtractorTask.settings.

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

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◆ getLogFilePathname()

String denoptim.fragmenter.ConformerExtractorTask.getLogFilePathname ( )

Returns: the pathname of the log file.

Definition at line 194 of file ConformerExtractorTask.java.

References denoptim.fragmenter.ConformerExtractorTask.logFilePathname.

Referenced by denoptim.fragmenter.ParallelConformerExtractionAlgorithm.createAndSubmitTasks().

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◆ getResultFile()

String denoptim.fragmenter.ConformerExtractorTask.getResultFile ( )

Returns: the pathname to the files collecting results

Definition at line 494 of file ConformerExtractorTask.java.

References denoptim.fragmenter.ConformerExtractorTask.results.

◆ populateListOfClusterizableFragments()

static boolean denoptim.fragmenter.ConformerExtractorTask.populateListOfClusterizableFragments	(	List< ClusterableFragment >	sample,
		Fragment	frag,
		Logger	logger,
		String	fragId
	)

static

Tries to add a fragment into a sample of isomorphic fragments.

Looks for an isomorphism to define a consistent ordering of FragIsomorphNode that allows clustering of fragments.

Parameters

sample	the collection of isomorphic fragments. Can be empty, in which case, we just add the fragment into this list.
frag	the fragment that we try to add to the sample.
logger	where any log should be posted.
fragId	a string identifying the fragment. Typically the index in a list of fragments.

Returns: true if the fragment has been added to the sample of false if no isomorphism could be found and, therefore, the fragment is not added to the sample.

Definition at line 400 of file ConformerExtractorTask.java.

References denoptim.fragmenter.ClusterableFragment.getJGraphFragIsomorphism(), denoptim.fragmenter.FragmentAlignement.getLowestRMSDMapping(), denoptim.fragmenter.ConformerExtractorTask.logger, denoptim.fragmenter.ConformerExtractorTask.sample, and denoptim.fragmenter.ClusterableFragment.setOrderOfNodes().

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

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