gmx::TrajectoryAnalysisModuleData Class Reference

#include <gromacs/trajectoryanalysis/analysismodule.h>

Inheritance diagram for gmx::TrajectoryAnalysisModuleData:

Description

Base class for thread-local data storage during trajectory analysis.

Thread-local storage of data handles and selections is implemented in this class; TrajectoryAnalysisModule instances can access the thread-local values in their TrajectoryAnalysisModule::analyzeFrame() method using dataHandle() and parallelSelection().

See Also

TrajectoryAnalysisModule::startFrames()

TrajectoryAnalysisModule::analyzeFrame()

TrajectoryAnalysisModule::finishFrames()

Examples:

template.cpp.

Classes
class	Impl
	Private implementation class for TrajectoryAnalysisModuleData. More...

Public Member Functions
virtual void	finish ()=0
	Performs any finishing actions after all frames have been processed. More...
AnalysisDataHandle	dataHandle (const AnalysisData &data)
	Returns a data handle for a given dataset. More...

Static Public Member Functions
static Selection	parallelSelection (const Selection &selection)
	Returns a selection that corresponds to the given selection. More...
static SelectionList	parallelSelections (const SelectionList &selections)
	Returns a set of selection that corresponds to the given selections. More...

Protected Member Functions
	TrajectoryAnalysisModuleData (TrajectoryAnalysisModule *module, const AnalysisDataParallelOptions &opt, const SelectionCollection &selections)
	Initializes thread-local storage for data handles and selections. More...
void	finishDataHandles ()
	Calls finishData() on all data handles. More...

Constructor & Destructor Documentation

gmx::TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData ( TrajectoryAnalysisModule *  module, const AnalysisDataParallelOptions &  opt, const SelectionCollection &  selections  )

protected

Initializes thread-local storage for data handles and selections.

Parameters

[in]	module	Analysis module to use for data objects.
[in]	opt	Data parallelization options.
[in]	selections	Thread-local selection collection.

Exceptions

std::bad_alloc	if out of memory.
unspecified	Can throw any exception thrown by AnalysisData::startData().

Calls AnalysisData::startData() on all data objects registered with TrajectoryAnalysisModule::registerAnalysisDataset() in module. The handles are accessible through dataHandle().

Member Function Documentation

AnalysisDataHandle gmx::TrajectoryAnalysisModuleData::dataHandle

(

const AnalysisData &

data

)

Returns a data handle for a given dataset.

Parameters

[in]

data

Analysis data object.

Returns

Data handle for data stored in this thread-local data.

data should have previously been registered with TrajectoryAnalysisModule::registerAnalysisDataset(). If data has zero columns in all data sets, the returned data handle is invalid.

Does not throw.

Examples:

template.cpp.

virtual void gmx::TrajectoryAnalysisModuleData::finish ( )

pure virtual

Performs any finishing actions after all frames have been processed.

Exceptions

unspecified

Implementation may throw exceptions to indicate errors.

This function is called immediately before the destructor, after TrajectoryAnalysisModule::finishFrames(). Derived classes should implement any final operations that need to be done after successful analysis. All implementations should call finishDataHandles().

Implemented in gmx::analysismodules::anonymous_namespace{sasa.cpp}::SasaModuleData, gmx::analysismodules::anonymous_namespace{rdf.cpp}::RdfModuleData, gmx::analysismodules::anonymous_namespace{pairdist.cpp}::PairDistanceModuleData, and gmx::anonymous_namespace{analysismodule.cpp}::TrajectoryAnalysisModuleDataBasic.

void gmx::TrajectoryAnalysisModuleData::finishDataHandles ( )

protected

Calls finishData() on all data handles.

Exceptions

unspecified

Can throw any exception thrown by AnalysisDataHandle::finishData().

This function should be called from the implementation of finish() in all subclasses.

Selection gmx::TrajectoryAnalysisModuleData::parallelSelection ( const Selection &  selection )

static

Returns a selection that corresponds to the given selection.

Parameters

[in]

selection

Global selection object.

Returns

Selection object corresponding to this thread-local data.

selection is the selection object that was obtained from SelectionOption. The return value is the corresponding selection in the selection collection with which this data object was constructed with.

Does not throw.

Examples:

template.cpp.

SelectionList gmx::TrajectoryAnalysisModuleData::parallelSelections ( const SelectionList &  selections )

static

Returns a set of selection that corresponds to the given selections.

Exceptions

std::bad_alloc

if out of memory.

Works as parallelSelection(), but for a list of selections at once.

See Also

parallelSelection()

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

• api/legacy/include/gromacs/trajectoryanalysis/analysismodule.h
• src/gromacs/trajectoryanalysis/analysismodule.cpp