#include <gromacs/trajectoryanalysis/runnercommon.h>

Description

Implements common trajectory analysis runner functionality.

As there is currently only one runner (TrajectoryAnalysisCommandLineRunner), the division of responsibilities is not yet very clear.

Public Member Functions
	TrajectoryAnalysisRunnerCommon (TrajectoryAnalysisSettings *settings)
	Initializes a new runner helper. More...

ITopologyProvider *	topologyProvider ()
	Returns a topology provider for SelectionOptionBehavior.

void	initOptions (IOptionsContainer options, TimeUnitBehavior timeUnitBehavior)
	Initializes common options for trajectory analysis. More...

void	optionsFinished ()
	Processes common option values after they have been parsed.

void	initTopology ()
	Load topology information if provided and/or required.

void	initFirstFrame ()
	Reads the first frame from the trajectory. More...

void	initFrameIndexGroup ()
	Initializes the index in frame() that specifies the atoms contained. More...

bool	readNextFrame ()
	Reads the next frame from the trajectory. More...

void	initFrame ()
	Performs common initialization for the currently loaded frame. More...

bool	hasTrajectory () const
	Returns true if input data comes from a trajectory.

const TopologyInformation &	topologyInformation () const
	Returns the topology information object.

t_trxframe &	frame () const
	Returns the currently loaded frame.

Constructor & Destructor Documentation

gmx::TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon ( TrajectoryAnalysisSettings * settings )

explicit

Initializes a new runner helper.

Parameters

settings Settings object to use.

void gmx::TrajectoryAnalysisRunnerCommon::initFirstFrame ( )

Reads the first frame from the trajectory.

After this call, frame() returns the first frame.

void gmx::TrajectoryAnalysisRunnerCommon::initFrame ( )

Performs common initialization for the currently loaded frame.

Currently, makes molecules whole if requested.

void gmx::TrajectoryAnalysisRunnerCommon::initFrameIndexGroup ( )

Initializes the index in frame() that specifies the atoms contained.

Can be called after selections have been compiled.

void gmx::TrajectoryAnalysisRunnerCommon::initOptions	(	IOptionsContainer *	options,
		TimeUnitBehavior *	timeUnitBehavior
	)

Initializes common options for trajectory analysis.

Parameters

[in,out]	options	Options object to add the options to.
[in,out]	timeUnitBehavior	Time unit behavior to use for adding and handling the `-tu` option.

bool gmx::TrajectoryAnalysisRunnerCommon::readNextFrame ( )

Reads the next frame from the trajectory.

After this call, frame() returns the newly loaded frame.

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