void
TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
{
TrajectoryAnalysisSettings &settings = impl_->settings_;
// Add options for help.
options->addOption(BooleanOption("h").store(&impl_->bHelp_)
.description("Print help and quit"));
options->addOption(BooleanOption("hidden").store(&impl_->bShowHidden_)
.hidden()
.description("Show hidden options"));
options->addOption(BooleanOption("quiet").store(&impl_->bQuiet_)
.hidden()
.description("Hide options in normal run"));
// Add common file name arguments.
options->addOption(FileNameOption("f")
.filetype(eftTrajectory).inputFile()
.store(&impl_->trjfile_)
.defaultBasename("traj")
.description("Input trajectory or single configuration"));
options->addOption(FileNameOption("s")
.filetype(eftTopology).inputFile()
.store(&impl_->topfile_)
.defaultBasename("topol")
.description("Input structure"));
options->addOption(FileNameOption("n")
.filetype(eftIndex).inputFile()
.store(&impl_->ndxfile_)
.defaultBasename("index")
.description("Extra index groups"));
options->addOption(SelectionFileOption("sf"));
// Add options for trajectory time control.
options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
.description("First frame (%t) to read from trajectory"));
options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
.description("Last frame (%t) to read from trajectory"));
options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
.description("Only use frame if t MOD dt == first time (%t)"));
// Add time unit option.
settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
// Add plot options.
settings.impl_->plotSettings.addOptions(options);
// Add common options for trajectory processing.
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
{
options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
.description("Make molecules whole for each frame"));
}
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
{
options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
.description("Use periodic boundary conditions for distance calculation"));
}
}
void
TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
TimeUnitBehavior *timeUnitBehavior)
{
TrajectoryAnalysisSettings &settings = impl_->settings_;
// Add common file name arguments.
options->addOption(FileNameOption("f")
.filetype(eftTrajectory).inputFile()
.store(&impl_->trjfile_)
.defaultBasename("traj")
.description("Input trajectory or single configuration"));
options->addOption(FileNameOption("s")
.filetype(eftTopology).inputFile()
.store(&impl_->topfile_)
.defaultBasename("topol")
.description("Input structure"));
// Add options for trajectory time control.
options->addOption(DoubleOption("b")
.store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
.timeValue()
.description("First frame (%t) to read from trajectory"));
options->addOption(DoubleOption("e")
.store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
.timeValue()
.description("Last frame (%t) to read from trajectory"));
options->addOption(DoubleOption("dt")
.store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
.timeValue()
.description("Only use frame if t MOD dt == first time (%t)"));
// Add time unit option.
timeUnitBehavior->setTimeUnitFromEnvironment();
timeUnitBehavior->addTimeUnitOption(options, "tu");
timeUnitBehavior->setTimeUnitStore(&impl_->settings_.impl_->timeUnit);
options->addOption(SelectionOption("fgroup")
.store(&impl_->trajectoryGroup_)
.onlySortedAtoms().onlyStatic()
.description("Atoms stored in the trajectory file "
"(if not set, assume first N atoms)"));
// Add plot options.
settings.impl_->plotSettings.initOptions(options);
// Add common options for trajectory processing.
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
{
options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
.description("Make molecules whole for each frame"));
}
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
{
options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
.description("Use periodic boundary conditions for distance calculation"));
}
}