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"));
}
}
void
Distance::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
{
static const char *const desc[] = {
"g_dist can calculate the distance between two positions as",
"a function of time. The total distance and its",
"x, y and z components are plotted."
};
options->setDescription(concatenateStrings(desc));
options->addOption(FileNameOption("o").filetype(eftPlot).outputFile()
.store(&fnDist_).defaultBasename("dist")
.description("Computed distances"));
options->addOption(SelectionOption("select").required().valueCount(2)
.store(sel_));
}
void
Angle::initOptions(Options *options, TrajectoryAnalysisSettings * /*settings*/)
{
static const char *const desc[] = {
"g_angle computes different types of angles between vectors.",
"It supports both vectors defined by two positions and normals of",
"planes defined by three positions.",
"The z axis or the local normal of a sphere can also be used as",
"one of the vectors.",
"There are also convenience options 'angle' and 'dihedral' for",
"calculating bond angles and dihedrals defined by three/four",
"positions.[PAR]",
"The type of the angle is specified with [TT]-g1[tt] and [TT]-g2[tt].",
"If [TT]-g1[tt] is [TT]angle[tt] or [TT]dihedral[tt], [TT]-g2[tt]",
"should not be specified.",
"In this case, [TT]-group1[tt] should specify one selection,",
"and it should contain triplets or quartets of positions that define",
"the angles to be calculated.[PAR]",
"If [TT]-g1[tt] is [TT]vector[tt] or [TT]plane[tt], [TT]-group1[tt]",
"should specify a selection that has either pairs ([TT]vector[tt])",
"or triplets ([TT]plane[tt]) of positions. For vectors, the positions",
"set the endpoints of the vector, and for planes, the three positions",
"are used to calculate the normal of the plane. In both cases,",
"[TT]-g2[tt] specifies the other vector to use (see below).[PAR]",
"With [TT]-g2 vector[tt] or [TT]-g2 plane[tt], [TT]-group2[tt] should",
"specify another set of vectors. Both selections should specify the",
"same number of vectors.[PAR]",
"With [TT]-g2 sphnorm[tt], [TT]-group2[tt] should specify a single",
"position that is the center of the sphere. The second vector is then",
"calculated as the vector from the center to the midpoint of the",
"positions specified by [TT]-group1[tt].[PAR]",
"With [TT]-g2 z[tt], [TT]-group2[tt] is not necessary, and angles",
"between the first vectors and the positive Z axis are calculated.[PAR]",
"With [TT]-g2 t0[tt], [TT]-group2[tt] is not necessary, and angles",
"are calculated from the vectors as they are in the first frame.[PAR]",
"There are two options for output:",
"[TT]-oav[tt] writes an xvgr file with the time and the average angle",
"for each frame.",
"[TT]-oall[tt] writes all the individual angles."
/* TODO: Consider if the dump option is necessary and how to best
* implement it.
"[TT]-od[tt] can be used to dump all the individual angles,",
"each on a separate line. This format is better suited for",
"further processing, e.g., if angles from multiple runs are needed."
*/
};
static const char *const cGroup1TypeEnum[] =
{ "angle", "dihedral", "vector", "plane" };
static const char *const cGroup2TypeEnum[] =
{ "none", "vector", "plane", "t0", "z", "sphnorm" };
options->setDescription(concatenateStrings(desc));
options->addOption(FileNameOption("oav").filetype(eftPlot).outputFile()
.store(&fnAverage_).defaultBasename("angaver")
.description("Average angles as a function of time"));
options->addOption(FileNameOption("oall").filetype(eftPlot).outputFile()
.store(&fnAll_).defaultBasename("angles")
.description("All angles as a function of time"));
// TODO: Add histogram output.
options->addOption(StringOption("g1").enumValue(cGroup1TypeEnum)
.defaultEnumIndex(0).store(&g1type_)
.description("Type of analysis/first vector group"));
options->addOption(StringOption("g2").enumValue(cGroup2TypeEnum)
.defaultEnumIndex(0).store(&g2type_)
.description("Type of second vector group"));
// TODO: Allow multiple angles to be computed in one invocation.
// Most of the code already supports it, but requires a solution for
// Redmine issue #1010.
// TODO: Consider what is the best way to support dynamic selections.
// Again, most of the code already supports it, but it needs to be
// considered how should -oall work, and additional checks should be added.
sel1info_ = options->addOption(SelectionOption("group1")
.required().onlyStatic().storeVector(&sel1_)
.description("First analysis/vector selection"));
sel2info_ = options->addOption(SelectionOption("group2")
.onlyStatic().storeVector(&sel2_)
.description("Second analysis/vector selection"));
}
Options *
Angle::initOptions(TrajectoryAnalysisSettings *settings)
{
static const char *const desc[] = {
"g_angle computes different types of angles between vectors.",
"It supports both vectors defined by two positions and normals of",
"planes defined by three positions.",
"The z axis or the local normal of a sphere can also be used as",
"one of the vectors.",
"There are also convenience options 'angle' and 'dihedral' for",
"calculating bond angles and dihedrals defined by three/four",
"positions.[PAR]",
"The type of the angle is specified with [TT]-g1[tt] and [TT]-g2[tt].",
"If [TT]-g1[tt] is [TT]angle[tt] or [TT]dihedral[tt], [TT]-g2[tt]",
"should not be specified.",
"In this case, one selection is required, and it should contain",
"triplets or quartets of positions that define the angles to be",
"calculated.",
"If [TT]-g1[tt] is not [TT]angle[tt] or [TT]dihedral[tt], [TT]-g2[tt]",
"should not be [TT]none[tt], and the two options define two vectors",
"for the calculation. For vectors ([TT]vector[tt]), a selection with",
"pairs of positions is required, and for planes ([TT]plane[tt]),",
"triplets of positions are required.",
"If both vectors are specified by positions, the number of vectors",
"should be the same in both selections.",
"[TT]-g2 sphnorm[tt] requires a reference selection that defines",
"the center of the sphere.",
"[TT]-g2 z[tt] does not require any selection.[PAR]",
"With [TT]-split1[tt], the positions for [TT]-g1[tt] are specified",
"using N separate selections with M positions each, instead of the",
"default M*N positions in one selection.",
"[TT]-split2[tt] does the same for [TT]-g2[tt].[PAR]",
"There are two options for output:",
"[TT]-o[tt] writes an xvgr file with the time and the average angle",
"for each frame.",
"With [TT]-all[tt], also the individual angles are written (only",
"supported for static selections).",
"[TT]-od[tt] can be used to dump all the individual angles,",
"each on a separate line. This format is better suited for",
"further processing, e.g., if angles from multiple runs are needed.",
NULL
};
static const char *const cGroup1TypeEnum[] =
{ "angle", "dihedral", "vector", "plane", NULL };
static const char *const cGroup2TypeEnum[] =
{ "none", "vector", "plane", "t0", "z", "sphnorm", NULL };
_options.setDescription(desc);
_options.addOption(FileNameOption("o").filetype(eftPlot).writeOnly()
.store(&_fnAngle).defaultValueIfSet("angle"));
_options.addOption(FileNameOption("od").filetype(eftPlot).writeOnly()
.store(&_fnDump).defaultValueIfSet("angdump"));
_options.addOption(StringOption("g1").enumValue(cGroup1TypeEnum)
.defaultEnumIndex(0).store(&_g1type)
.description("Type of analysis/first vector group"));
_options.addOption(StringOption("g2").enumValue(cGroup2TypeEnum)
.defaultEnumIndex(0).store(&_g2type)
.description("Type of second vector group"));
_options.addOption(BooleanOption("split1").store(&_bSplit1)
.description("Each position of first group in separate selection"));
_options.addOption(BooleanOption("split2").store(&_bSplit2)
.description("Each position of second group in separate selection"));
_options.addOption(BooleanOption("multi").store(&_bMulti)
.description("Analyze multiple sets of angles/dihedrals"));
_options.addOption(BooleanOption("all").store(&_bAll)
.description("Print individual angles together with the average"));
_options.addOption(BooleanOption("dumpd").store(&_bDumpDist)
.description("Write also distances with -od"));
_options.addOption(SelectionOption("group1").multiValue().required()
.dynamicOnlyWhole().storeVector(&_sel1).getAdjuster(&_sel1Adj)
.description("First analysis/vector selection"));
_options.addOption(SelectionOption("group2").multiValue()
.dynamicOnlyWhole().storeVector(&_sel2).getAdjuster(&_sel2Adj)
.description("Second analysis/vector selection"));
return &_options;
}
