Fragments a list of chemical systems by running parallel fragmentation tasks. More...

Inheritance diagram for denoptim.fragmenter.ParallelFragmentationAlgorithm:

Collaboration diagram for denoptim.fragmenter.ParallelFragmentationAlgorithm:

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

Public Member Functions inherited from denoptim.task.ParallelAsynchronousTaskExecutor
	ParallelAsynchronousTaskExecutor (int numberOfTasks, Logger logger)
	Constructor. More...

void	stopRun ()
	Stops all subtasks and shutdown executor. More...

void	run () throws DENOPTIMException, IOException
	Run the parallelized task. More...

Protected Member Functions
boolean	doPreFlightOperations ()

void	createAndSubmitTasks ()
	Implementations of this method must call the `submitTask(Task, String)` method to actually send the task to the executor and eventually start it. More...

boolean	doPostFlightOperations ()

Protected Member Functions inherited from denoptim.task.ParallelAsynchronousTaskExecutor
boolean	subtaskHasException ()
	Looks for exceptions in the subtasks and, if any, store its reference locally to allow reporting it back from the main thread. More...

Throwable	getExceptionFromSubTask ()

boolean	allTasksCompleted ()
	Check for completion of all subtasks. More...

void	submitTask (Task task, String logFilePathname)

abstract void	createAndSubmitTasks ()
	Implementations of this method must call the `submitTask(Task, String)` method to actually send the task to the executor and eventually start it. More...

abstract boolean	doPostFlightOperations ()

abstract boolean	doPreFlightOperations ()

Static Protected Member Functions
static List< File >	getFilesCollectingIsomorphicFamilyChampions (File workDir)

Static Package Functions
static void	splitInputForThreads (FragmenterParameters settings, IteratingAtomContainerReader reader)
	Splits the input data (from `FragmenterParameters`) into batches suitable for parallel batch processing. More...

static String	getStructureFileNameBatch (FragmenterParameters settings, int i)
	Builds the pathname of the structure file generated for one of the parallel threads. More...

Static Private Member Functions
static boolean	getFormulaForMol (IAtomContainer mol, int index, LinkedHashMap< String, String > formulae)
	Takes the molecular formula from the given list of formulae and using the 'Title' property of the index or the molecule. More...

Private Attributes
File[]	structures
	Collection of files with input. More...

FragmenterParameters	settings = null
	All settings controlling the tasks executed by this class. More...

Additional Inherited Members
Protected Attributes inherited from denoptim.task.ParallelAsynchronousTaskExecutor
final List< Object >	results
	List of object returned by completed tasks. More...

Package Attributes inherited from denoptim.task.ParallelAsynchronousTaskExecutor
final ThreadPoolExecutor	tpe
	Asynchronous tasks manager. More...

Detailed Description

Fragments a list of chemical systems by running parallel fragmentation tasks.

Author: Marco Foscato

Definition at line 56 of file ParallelFragmentationAlgorithm.java.

Constructor & Destructor Documentation

◆ ParallelFragmentationAlgorithm()

denoptim.fragmenter.ParallelFragmentationAlgorithm.ParallelFragmentationAlgorithm ( FragmenterParameters settings )

Constructor.

Definition at line 76 of file ParallelFragmentationAlgorithm.java.

References denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.fragmenter.FragmenterParameters.getNumTasks(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.settings.

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Member Function Documentation

◆ createAndSubmitTasks()

void denoptim.fragmenter.ParallelFragmentationAlgorithm.createAndSubmitTasks ( )

protected

Implementations of this method must call the submitTask(Task, String) method to actually send the task to the executor and eventually start it.

Reimplemented from denoptim.task.ParallelAsynchronousTaskExecutor.

Definition at line 123 of file ParallelFragmentationAlgorithm.java.

References denoptim.fragmenter.FragmenterTask.getLogFilePathname(), denoptim.programs.fragmenter.FragmenterParameters.getNumTasks(), denoptim.fragmenter.ParallelFragmentationAlgorithm.settings, denoptim.fragmenter.ParallelFragmentationAlgorithm.structures, and denoptim.task.ParallelAsynchronousTaskExecutor.submitTask().

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◆ doPostFlightOperations()

boolean denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations ( )

protected

Reimplemented from denoptim.task.ParallelAsynchronousTaskExecutor.

Definition at line 141 of file ParallelFragmentationAlgorithm.java.

References denoptim.io.DenoptimIO.appendTxtFiles(), denoptim.programs.fragmenter.FragmenterParameters.doExtactRepresentativeConformer, denoptim.programs.fragmenter.FragmenterParameters.doFragmentation, denoptim.programs.fragmenter.FragmenterParameters.doManageIsomorphicFamilies, denoptim.fragmenter.ParallelFragmentationAlgorithm.getFilesCollectingIsomorphicFamilyChampions(), denoptim.fragmenter.FragmenterTask.getFragmentsFileName(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.programs.fragmenter.FragmenterParameters.getNumTasks(), denoptim.fragmenter.ParallelConformerExtractionAlgorithm.getResults(), denoptim.fragmenter.FragmenterTask.getResultsFileName(), denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.files.FileFormat.MOLSDF, denoptim.task.ParallelAsynchronousTaskExecutor.results, denoptim.task.ParallelAsynchronousTaskExecutor.run(), denoptim.fragmenter.ParallelFragmentationAlgorithm.settings, and denoptim.constants.DENOPTIMConstants.TMPFRAGFILEFORMAT.

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◆ doPreFlightOperations()

boolean denoptim.fragmenter.ParallelFragmentationAlgorithm.doPreFlightOperations ( )

protected

Reimplemented from denoptim.task.ParallelAsynchronousTaskExecutor.

Definition at line 84 of file ParallelFragmentationAlgorithm.java.

References denoptim.io.IteratingAtomContainerReader.getIteratorType(), denoptim.programs.fragmenter.FragmenterParameters.getNumTasks(), denoptim.fragmenter.ParallelFragmentationAlgorithm.getStructureFileNameBatch(), denoptim.programs.fragmenter.FragmenterParameters.getStructuresFile(), denoptim.fragmenter.ParallelFragmentationAlgorithm.settings, denoptim.programs.fragmenter.FragmenterParameters.setWorkingIn3D(), denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.structures.

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◆ getFilesCollectingIsomorphicFamilyChampions()

static List< File > denoptim.fragmenter.ParallelFragmentationAlgorithm.getFilesCollectingIsomorphicFamilyChampions ( File workDir )

staticprotected

Definition at line 259 of file ParallelFragmentationAlgorithm.java.

References denoptim.constants.DENOPTIMConstants.MWSLOTFRAGSFILENAMEROOT, and denoptim.constants.DENOPTIMConstants.MWSLOTFRAGSUNQFILENANEEND.

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

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◆ getFormulaForMol()

static boolean denoptim.fragmenter.ParallelFragmentationAlgorithm.getFormulaForMol	(	IAtomContainer	mol,
		int	index,
		LinkedHashMap< String, String >	formulae
	)

staticprivate

Takes the molecular formula from the given list of formulae and using the 'Title' property of the index or the molecule.

The formula taken from the list in argument is then placed among the properties of the chemical object.

Definition at line 437 of file ParallelFragmentationAlgorithm.java.

References denoptim.constants.DENOPTIMConstants.FORMULASTR.

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

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◆ getStructureFileNameBatch()

static String denoptim.fragmenter.ParallelFragmentationAlgorithm.getStructureFileNameBatch	(	FragmenterParameters	settings,
		int	i
	)

staticpackage

Builds the pathname of the structure file generated for one of the parallel threads.

Parameters

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

Returns: the pathname

Definition at line 422 of file ParallelFragmentationAlgorithm.java.

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

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

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◆ splitInputForThreads()

static void denoptim.fragmenter.ParallelFragmentationAlgorithm.splitInputForThreads	(	FragmenterParameters	settings,
		IteratingAtomContainerReader	reader
	)

staticpackage

Splits the input data (from FragmenterParameters) into batches suitable for parallel batch processing.

Since we have to read all the atom containers, we use this chance to do any preparation of the molecular representation (see FragmenterTools#prepareMolToFragmentation(IAtomContainer, FragmenterParameters, int)) and store the molecular formula in the property DENOPTIMConstants#FORMULASTR.

Exceptions