Task that performs the various steps in the process that prepares chemical structured to be chopped, chops them, and post-process the resulting fragments. More...

Inheritance diagram for denoptim.fragmenter.FragmenterTask:

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Public Member Functions
	FragmenterTask (File inputFile, FragmenterParameters settings, int id) throws SecurityException, IOException
	Create a task by giving the input file (i.e., containing structures to work with) and the configuration of the task. More...

String	getLogFilePathname ()

String	getResultFile ()

Object	call () throws Exception
	Performs the whatever work has to be done by this task. 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 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	getInputFileName (FragmenterParameters settings, int i)
	Builds the pathname of the structure file meant to be the input for this task. More...

static String	getConfirmedFormulaFileName (FragmenterParameters settings, int i)
	Builds the pathname of the structure file meant to hold structures that survive the comparison of structure's elemental analysis against the declared molecular formula. More...

static String	getPreFilteredFileName (FragmenterParameters settings, int i)
	Builds the pathname of the structure file meant to hold structures that survive the pre-filtering step, if any. More...

static String	getFragmentsFileName (FragmenterParameters settings, int i)
	Builds the pathname of the structure file meant to hold fragments resulting from this task. More...

static String	getFragmentsFileName (FragmenterParameters settings)
	Builds the pathname of the structure file meant to hold fragments resulting from all tasks. More...

static String	getResultsFileName (FragmenterParameters settings)
	Builds the pathname of the structure file meant to hold results that are not necessarily fragments. More...

Static Private Member Functions
static String	getLogFileName (FragmenterParameters settings, int i)
	Builds the pathname of the log file for this task. More...

Private Attributes
File	inputFile
	File containing the input for this task (i.e., a structure file) More...

File	preliminaryResults
	File containing the latest results, though not the final results. 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 performs the various steps in the process that prepares chemical structured to be chopped, chops them, and post-process the resulting fragments.

Each of the steps may or may not be part of the actual workflow, depending on the configurations given upon construction of the task. Note that preliminary adaptation of the molecular representations is expected to be done before calling this task. So the systems to fragment should have been already be processed by FragmenterTools#prepareMolToFragmentation(org.openscience.cdk.interfaces.IAtomContainer, FragmenterParameters, int) before starting this task.

Definition at line 46 of file FragmenterTask.java.

Constructor & Destructor Documentation

◆ FragmenterTask()

denoptim.fragmenter.FragmenterTask.FragmenterTask	(	File	inputFile,
		FragmenterParameters	settings,
		int	id
	)		throws SecurityException, IOException

Create a task by giving the input file (i.e., containing structures to work with) and the configuration of the task.

Note we start a task-specific logger that prints to a task-specific file.

Parameters

inputFile	the source of structures to work with.
settings	the configuration of the task.
id	identifier of the thread running this task.

Exceptions

SecurityException
IOException

Definition at line 91 of file FragmenterTask.java.

References denoptim.fragmenter.FragmenterTask.getLogFileName(), denoptim.programs.RunTimeParameters.getLogger(), denoptim.utils.TaskUtils.getUniqueTaskIndex(), denoptim.task.Task.id, denoptim.fragmenter.FragmenterTask.inputFile, denoptim.fragmenter.FragmenterTask.logFilePathname, denoptim.fragmenter.FragmenterTask.logger, and denoptim.fragmenter.FragmenterTask.settings.

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Member Function Documentation

◆ call()

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

Performs the whatever work has to be done by this task.

Definition at line 248 of file FragmenterTask.java.

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◆ getConfirmedFormulaFileName()

static String denoptim.fragmenter.FragmenterTask.getConfirmedFormulaFileName	(	FragmenterParameters	settings,
		int	i
	)

staticpackage

Builds the pathname of the structure file meant to hold structures that survive the comparison of structure's elemental analysis against the declared molecular formula.

Parameters

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

Returns: the pathname

Definition at line 163 of file FragmenterTask.java.

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

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

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◆ getFragmentsFileName() [1/2]

static String denoptim.fragmenter.FragmenterTask.getFragmentsFileName ( FragmenterParameters settings )

staticpackage

Builds the pathname of the structure file meant to hold fragments resulting from all tasks.

Parameters

settings settings we work with.

Returns: the pathname

Definition at line 207 of file FragmenterTask.java.

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

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◆ getFragmentsFileName() [2/2]

static String denoptim.fragmenter.FragmenterTask.getFragmentsFileName	(	FragmenterParameters	settings,
		int	i
	)

staticpackage

Builds the pathname of the structure file meant to hold fragments resulting from this task.

Parameters

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

Returns: the pathname

Definition at line 193 of file FragmenterTask.java.

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

Referenced by denoptim.fragmenter.FragmenterTask.call(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations().

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◆ getInputFileName()

static String denoptim.fragmenter.FragmenterTask.getInputFileName	(	FragmenterParameters	settings,
		int	i
	)

staticpackage

Builds the pathname of the structure file meant to be the input for this task.

Parameters

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

Returns: the pathname

Definition at line 127 of file FragmenterTask.java.

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

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◆ getLogFileName()

static String denoptim.fragmenter.FragmenterTask.getLogFileName	(	FragmenterParameters	settings,
		int	i
	)

staticprivate

Builds the pathname of the log file for this task.

Parameters

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

Returns: the pathname

Definition at line 235 of file FragmenterTask.java.

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

Referenced by denoptim.fragmenter.FragmenterTask.FragmenterTask().

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◆ getLogFilePathname()

String denoptim.fragmenter.FragmenterTask.getLogFilePathname ( )

Returns: the pathname of the log file.

Definition at line 138 of file FragmenterTask.java.

References denoptim.fragmenter.FragmenterTask.logFilePathname.

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

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◆ getPreFilteredFileName()

static String denoptim.fragmenter.FragmenterTask.getPreFilteredFileName	(	FragmenterParameters	settings,
		int	i
	)

staticpackage

Builds the pathname of the structure file meant to hold structures that survive the pre-filtering step, if any.

Parameters

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

Returns: the pathname

Definition at line 178 of file FragmenterTask.java.

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

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

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◆ getResultFile()

String denoptim.fragmenter.FragmenterTask.getResultFile ( )

Returns: the pathname to the file collecting results

Definition at line 148 of file FragmenterTask.java.

References denoptim.fragmenter.FragmenterTask.results.

◆ getResultsFileName()

static String denoptim.fragmenter.FragmenterTask.getResultsFileName ( FragmenterParameters settings )

staticpackage

Builds the pathname of the structure file meant to hold results that are not necessarily fragments.

Parameters

settings settings we work with.

Returns: the pathname

Definition at line 221 of file FragmenterTask.java.

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

Referenced by denoptim.fragmenter.ConformerExtractorTask.call(), and denoptim.fragmenter.ParallelFragmentationAlgorithm.doPostFlightOperations().

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Member Data Documentation

◆ inputFile

File denoptim.fragmenter.FragmenterTask.inputFile

private

File containing the input for this task (i.e., a structure file)

Definition at line 51 of file FragmenterTask.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), and denoptim.fragmenter.FragmenterTask.FragmenterTask().

◆ logFilePathname

String denoptim.fragmenter.FragmenterTask.logFilePathname = "unset"

private

Pathname to thread-specific log.

Definition at line 77 of file FragmenterTask.java.

Referenced by denoptim.fragmenter.FragmenterTask.FragmenterTask(), and denoptim.fragmenter.FragmenterTask.getLogFilePathname().

◆ logger

Logger denoptim.fragmenter.FragmenterTask.logger = null

private

Logger for this task.

Definition at line 72 of file FragmenterTask.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), and denoptim.fragmenter.FragmenterTask.FragmenterTask().

◆ preliminaryResults

File denoptim.fragmenter.FragmenterTask.preliminaryResults

private

File containing the latest results, though not the final results.

For instance, the results of an intermediate step in the task.

Definition at line 57 of file FragmenterTask.java.

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

◆ results

String denoptim.fragmenter.FragmenterTask.results = null

protected

The data structure holding the results of this task.

Definition at line 62 of file FragmenterTask.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), and denoptim.fragmenter.FragmenterTask.getResultFile().

◆ settings

FragmenterParameters denoptim.fragmenter.FragmenterTask.settings

protected

Settings for the calculation of the fitness.

Definition at line 67 of file FragmenterTask.java.

Referenced by denoptim.fragmenter.FragmenterTask.call(), denoptim.fragmenter.FragmenterTask.FragmenterTask(), denoptim.fragmenter.FragmenterTask.getConfirmedFormulaFileName(), denoptim.fragmenter.FragmenterTask.getFragmentsFileName(), denoptim.fragmenter.FragmenterTask.getInputFileName(), denoptim.fragmenter.FragmenterTask.getLogFileName(), denoptim.fragmenter.FragmenterTask.getPreFilteredFileName(), and denoptim.fragmenter.FragmenterTask.getResultsFileName().

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

/github/workspace/src/main/java/denoptim/fragmenter/FragmenterTask.java

Public Member Functions

Protected Attributes

Static Package Functions

Static Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FragmenterTask()

Member Function Documentation

◆ call()

◆ getConfirmedFormulaFileName()

◆ getFragmentsFileName() [1/2]

◆ getFragmentsFileName() [2/2]

◆ getInputFileName()

◆ getLogFileName()

◆ getLogFilePathname()

◆ getPreFilteredFileName()

◆ getResultFile()

◆ getResultsFileName()

Member Data Documentation

◆ inputFile

◆ logFilePathname

◆ logger

◆ preliminaryResults

◆ results

◆ settings