Runs threads that extract the most representative conformer of fragments given as input. More...

Inheritance diagram for denoptim.fragmenter.ParallelConformerExtractionAlgorithm:

Collaboration diagram for denoptim.fragmenter.ParallelConformerExtractionAlgorithm:

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

List< String >	getResults ()
	Returns the list of pathnames collecting the most representative conformers, as defined by the settings (i.e., either cluster centroids or fragment closest to the centroids). 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 ()

Private Attributes
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

Runs threads that extract the most representative conformer of fragments given as input.

Author: Marco Foscato

Definition at line 40 of file ParallelConformerExtractionAlgorithm.java.

Constructor & Destructor Documentation

◆ ParallelConformerExtractionAlgorithm()

denoptim.fragmenter.ParallelConformerExtractionAlgorithm.ParallelConformerExtractionAlgorithm ( FragmenterParameters settings )

Constructor.

We expect to run this from ParallelFragmentationAlgorithm.

Definition at line 55 of file ParallelConformerExtractionAlgorithm.java.

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

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Member Function Documentation

◆ createAndSubmitTasks()

void denoptim.fragmenter.ParallelConformerExtractionAlgorithm.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 70 of file ParallelConformerExtractionAlgorithm.java.

References denoptim.fragmenter.ConformerExtractorTask.getLogFilePathname(), denoptim.programs.RunTimeParameters.getWorkDirectory(), denoptim.io.DenoptimIO.readVertexes(), denoptim.fragmenter.ParallelConformerExtractionAlgorithm.settings, denoptim.task.ParallelAsynchronousTaskExecutor.submitTask(), and denoptim.graph.Vertex.BBType.UNDEFINED.

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◆ doPostFlightOperations()

boolean denoptim.fragmenter.ParallelConformerExtractionAlgorithm.doPostFlightOperations ( )

protected

Reimplemented from denoptim.task.ParallelAsynchronousTaskExecutor.

Definition at line 106 of file ParallelConformerExtractionAlgorithm.java.

◆ doPreFlightOperations()

boolean denoptim.fragmenter.ParallelConformerExtractionAlgorithm.doPreFlightOperations ( )

protected

Reimplemented from denoptim.task.ParallelAsynchronousTaskExecutor.

Definition at line 63 of file ParallelConformerExtractionAlgorithm.java.

◆ getResults()

List< String > denoptim.fragmenter.ParallelConformerExtractionAlgorithm.getResults ( )

Returns the list of pathnames collecting the most representative conformers, as defined by the settings (i.e., either cluster centroids or fragment closest to the centroids).