Gromacs
5.1
|
#include <gromacs/trajectoryanalysis/runnercommon.h>
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... | |
void | initOptions (Options *options) |
Initializes common options for trajectory analysis. More... | |
void | scaleTimeOptions (Options *options) |
Scales time option values according to the time unit set. | |
void | optionsFinished (Options *options) |
Processes common option values after they have been parsed. More... | |
void | initIndexGroups (SelectionCollection *selections, bool bUseDefaults) |
Initialize index groups for selections. | |
void | doneIndexGroups (SelectionCollection *selections) |
Free memory allocated for index groups. | |
void | initTopology (SelectionCollection *selections) |
Load topology information if provided and/or required. | |
void | initFirstFrame () |
Reads the first frame from the trajectory. 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. | |
|
explicit |
Initializes a new runner helper.
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::initOptions | ( | Options * | options | ) |
Initializes common options for trajectory analysis.
[in,out] | options | Options object to add the options to. |
void gmx::TrajectoryAnalysisRunnerCommon::optionsFinished | ( | Options * | options | ) |
Processes common option values after they have been parsed.
[in,out] | options | Options object in which options are stored. |
bool gmx::TrajectoryAnalysisRunnerCommon::readNextFrame | ( | ) |
Reads the next frame from the trajectory.
After this call, frame() returns the newly loaded frame.