Tool to create fragments by chopping 2D/3D chemical structures. More...

Inheritance diagram for denoptim.programs.fragmenter.Fragmenter:

Collaboration diagram for denoptim.programs.fragmenter.Fragmenter:

Public Member Functions
	Fragmenter (File configFile, File workDir)
	Creates and configures the program task. More...

void	runProgram () throws Throwable

Public Member Functions inherited from denoptim.task.ProgramTask
	ProgramTask (File configFile, File workDir)
	Creates and configures the program task. More...

Object	call ()
	This method redirects the callable functionality to an abstract method (namely `ProgramTask#runProgram()`) to be specified by the implementations of this abstract class. More...

void	printErrorToFile ()
	Method that can be called to create a text file with the error triggered by any `Throwable` that can be thrown by the execution of the program. More...

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)

Protected Member Functions
void	handleThrowable ()
	Method to handle any `Throwable` originated from the `runProgram()` method. More...

Protected Member Functions inherited from denoptim.task.ProgramTask
void	handleThrowable ()
	Method to handle any `Throwable` originated from the `runProgram()` method. More...

void	stopLogger ()
	Stops the program-specific logger and releases the lock file on the logfile. More...

abstract void	runProgram () throws Throwable

Private Attributes
ParallelFragmentationAlgorithm	fragAlgorithm = null

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

Protected Attributes inherited from denoptim.task.ProgramTask
File	configFilePathName
	File containing configuration parameters for the program task. More...

String	loggerIdentifier = "none"
	Identifier of this program's logger. 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...

Detailed Description

Tool to create fragments by chopping 2D/3D chemical structures.

Author: Marco Foscato

Definition at line 38 of file Fragmenter.java.

Constructor & Destructor Documentation

◆ Fragmenter()

denoptim.programs.fragmenter.Fragmenter.Fragmenter	(	File	configFile,
		File	workDir
	)

Creates and configures the program task.

Parameters

configFile	the file containing the configuration parameters.
workDir	the file system location from which to run the program.

Definition at line 49 of file Fragmenter.java.

References denoptim.task.Task.workDir.

Member Function Documentation

◆ handleThrowable()

void denoptim.programs.fragmenter.Fragmenter.handleThrowable ( )

protected

Method to handle any Throwable originated from the runProgram() method.

This method can be overwritten to alter the behavior in case of specific needs.

Reimplemented from denoptim.task.ProgramTask.

Definition at line 87 of file Fragmenter.java.

References denoptim.programs.fragmenter.Fragmenter.fragAlgorithm, and denoptim.task.ParallelAsynchronousTaskExecutor.stopRun().

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◆ runProgram()

void denoptim.programs.fragmenter.Fragmenter.runProgram ( ) throws Throwable

Reimplemented from denoptim.task.ProgramTask.

Definition at line 57 of file Fragmenter.java.

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Member Data Documentation

◆ fragAlgorithm

ParallelFragmentationAlgorithm denoptim.programs.fragmenter.Fragmenter.fragAlgorithm = null

private

Definition at line 40 of file Fragmenter.java.

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

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

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

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members