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gmx::TrajectoryAnalysisRunnerCommon Class Reference

#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...
 
ITopologyProvidertopologyProvider ()
 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 TopologyInformationtopologyInformation () 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
settingsSettings object to use.

Member Function Documentation

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]optionsOptions object to add the options to.
[in,out]timeUnitBehaviorTime unit behavior to use for adding and handling the -tu option.
bool gmx::TrajectoryAnalysisRunnerCommon::readNextFrame ( )

Reads the next frame from the trajectory.

Returns
false if there were no more frames.

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


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