Gromacs
2025-dev-20241008-cf8b9ef
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#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... | |
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. | |
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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::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.
[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.