Description

Template class to serve as a basis for user analysis tools.

Examples:: template.cpp.

Public Member Functions
virtual void	initOptions (IOptionsContainer options, TrajectoryAnalysisSettings settings)
	Initializes options understood by the module. More...

virtual void	initAnalysis (const TrajectoryAnalysisSettings &settings, const TopologyInformation &top)
	Initializes the analysis. More...

virtual void	analyzeFrame (int frnr, const t_trxframe &fr, t_pbc pbc, TrajectoryAnalysisModuleData pdata)
	Analyzes a single frame. More...

virtual void	finishAnalysis (int nframes)
	Postprocesses data after frames have been read. More...

virtual void	writeOutput ()
	Writes output into files and/or standard output/error. More...

Public Member Functions inherited from gmx::TrajectoryAnalysisModule
virtual void	optionsFinished (TrajectoryAnalysisSettings *settings)
	Called after all option values have been set. More...

virtual void	initAfterFirstFrame (const TrajectoryAnalysisSettings &settings, const t_trxframe &fr)
	Performs additional initialization after reading the first frame. More...

virtual TrajectoryAnalysisModuleDataPointer	startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections)
	Starts the analysis of frames. More...

virtual void	finishFrames (TrajectoryAnalysisModuleData *pdata)
	Finishes the analysis of frames. More...

int	datasetCount () const
	Returns the number of datasets provided by the module. More...

const std::vector< std::string > &	datasetNames () const
	Returns a vector with the names of datasets provided by the module. More...

AbstractAnalysisData &	datasetFromIndex (int index) const
	Returns a pointer to the data set `index`. More...

AbstractAnalysisData &	datasetFromName (const char *name) const
	Returns a pointer to the data set with name `name`. More...

void	finishFrameSerial (int frameIndex)
	Processes data in AnalysisData objects in serial for each frame. More...

Additional Inherited Members
Protected Member Functions inherited from gmx::TrajectoryAnalysisModule
	TrajectoryAnalysisModule ()
	Initializes the dataset registration mechanism. More...

void	registerBasicDataset (AbstractAnalysisData data, const char name)
	Registers a dataset that exports data. More...

void	registerAnalysisDataset (AnalysisData data, const char name)
	Registers a parallelized dataset that exports data. More...

Member Function Documentation

void AnalysisTemplate::analyzeFrame	(	int	frnr,
		const t_trxframe &	fr,
		t_pbc *	pbc,
		TrajectoryAnalysisModuleData *	pdata
	)

virtual

Analyzes a single frame.

Parameters

[in]	frnr	Frame number, a zero-based index that uniquely identifies the frame.
[in]	fr	Current frame.
[in]	pbc	Periodic boundary conditions for `fr`.
[in,out]	pdata	Data structure for frame-local data.

This method is called once for each frame to be analyzed, and should analyze the positions provided in the selections. Data handles and selections should be obtained from the pdata structure.

For threaded analysis, this method is called asynchronously in different threads to analyze different frames. The pdata structure is one of the structures created with startFrames(), but no assumptions should be made about which of these data structures is used. It is guaranteed that two instances of analyzeFrame() are not running concurrently with the same pdata data structure. Any access to data structures not stored in pdata should be designed to be thread-safe.

Implements gmx::TrajectoryAnalysisModule.

Examples:: template.cpp.

void AnalysisTemplate::finishAnalysis ( int nframes )

virtual

Postprocesses data after frames have been read.

Parameters

[in] nframes Total number of frames processed.

This function is called after all finishFrames() calls have been called. nframes will equal the number of calls to analyzeFrame() that have occurred.

Implements gmx::TrajectoryAnalysisModule.

Examples:: template.cpp.

void AnalysisTemplate::initAnalysis	(	const TrajectoryAnalysisSettings &	settings,
		const TopologyInformation &	top
	)

virtual

Initializes the analysis.

Parameters

[in]	settings	Settings to pass to and from the module.
[in]	top	Topology information.

When this function is called, selections have been initialized based on user input, and a topology has been loaded if provided by the user. For dynamic selections, the selections have been evaluated to the largest possible selection, i.e., the selections passed to analyzeFrame() are always a subset of the selections provided here.

Implements gmx::TrajectoryAnalysisModule.

Examples:: template.cpp.

void AnalysisTemplate::initOptions	(	IOptionsContainer *	options,
		TrajectoryAnalysisSettings *	settings
	)

virtual

Initializes options understood by the module.

Parameters

[in,out]	options	Options object to add the options to.
[in,out]	settings	Settings to pass to and from the module.

This method is called first after the constructor, and it should add options understood by the module to options. Output values from options (including selections) should be stored in member variables.

In addition to initializing the options, this method can also provide information about the module's requirements using the settings object; see TrajectoryAnalysisSettings for more details.

If settings depend on the option values provided by the user, see optionsFinished().

Implements gmx::TrajectoryAnalysisModule.

Examples:: template.cpp.

void AnalysisTemplate::writeOutput ( )

virtual

Writes output into files and/or standard output/error.

All output from the module, excluding data written out for each frame during analyzeFrame(), should be confined into this function. This function is guaranteed to be called only after finishAnalysis().

Implements gmx::TrajectoryAnalysisModule.

Examples:: template.cpp.

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

share/template/template.cpp

Description

Public Member Functions

Additional Inherited Members

Member Function Documentation