Gromacs
2024.3
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#include <gromacs/trajectoryanalysis/analysissettings.h>
Trajectory analysis module configuration object.
This class is used by trajectory analysis modules to inform the caller about the requirements they have on the input (e.g., whether a topology is required, or whether PBC removal makes sense). It is also used to pass similar information back to the analysis module after parsing user input.
Having this functionality as a separate class makes the TrajectoryAnalysisModule interface much cleaner, and also reduces the need to change existing code when new options are added.
Methods in this class do not throw, except for the constructor, which may throw an std::bad_alloc.
Public Types | |
enum | { efRequireTop = 1 << 0, efUseTopX = 1 << 1, efUseTopV = 1 << 2, efNoUserPBC = 1 << 4, efNoUserRmPBC = 1 << 5 } |
Recognized flags. More... | |
Public Member Functions | |
TrajectoryAnalysisSettings () | |
Initializes default settings. | |
void | setOptionsModuleSettings (ICommandLineOptionsModuleSettings *settings) |
Injects command line options module settings for some methods to use. | |
TimeUnit | timeUnit () const |
Returns the time unit the user has requested. | |
const AnalysisDataPlotSettings & | plotSettings () const |
Returns common settings for analysis data plot modules. | |
unsigned long | flags () const |
Returns the currently set flags. | |
bool | hasFlag (unsigned long flag) const |
Tests whether a flag has been set. | |
bool | hasPBC () const |
Returns whether PBC should be used. More... | |
bool | hasRmPBC () const |
Returns whether molecules should be made whole. More... | |
int | frflags () const |
Returns the currently set frame flags. | |
void | setFlags (unsigned long flags) |
Sets flags. More... | |
void | setFlag (unsigned long flag, bool bSet=true) |
Sets or clears an individual flag. | |
void | setPBC (bool bPBC) |
Sets whether PBC are used. More... | |
void | setRmPBC (bool bRmPBC) |
Sets whether molecules are made whole. More... | |
void | setFrameFlags (int frflags) |
Sets flags that determine what to read from the trajectory. More... | |
void | setHelpText (const ArrayRef< const char *const > &help) |
Sets the help text for the module from string array. More... | |
Friends | |
class | TrajectoryAnalysisRunnerCommon |
anonymous enum |
Recognized flags.
Enumerator | |
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efRequireTop |
Forces loading of a topology file. If this flag is not specified, the topology file is loaded only if it is provided on the command line explicitly. |
efUseTopX |
Requests topology coordinates. If this flag is specified, the position coordinates loaded from the topology can be accessed, otherwise they are not loaded.
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efUseTopV |
Requests topology coordinates. If this flag is specified, the velocity coordinates loaded from the topology can be accessed, otherwise they are not loaded.
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efNoUserPBC |
Disallows the user from changing PBC handling. If this option is not specified, the analysis module (see TrajectoryAnalysisModule::analyzeFrame()) may be passed a NULL PBC structure, and it should be able to handle such a situation.
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efNoUserRmPBC |
Disallows the user from changing PBC removal.
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bool gmx::TrajectoryAnalysisSettings::hasPBC | ( | ) | const |
Returns whether PBC should be used.
Returns the value set with setPBC() and/or overridden by the user. The user-provided value can be accessed in TrajectoryAnalysisModule::optionsFinished(), and can be overridden with a call to setPBC().
bool gmx::TrajectoryAnalysisSettings::hasRmPBC | ( | ) | const |
Returns whether molecules should be made whole.
See hasPBC() for information on accessing or overriding the user-provided value.
void gmx::TrajectoryAnalysisSettings::setFlags | ( | unsigned long | flags | ) |
Sets flags.
Overrides any earlier set flags. By default, no flags are set.
void gmx::TrajectoryAnalysisSettings::setFrameFlags | ( | int | frflags | ) |
Sets flags that determine what to read from the trajectory.
[in] | frflags | Flags for what to read from the trajectory file. |
If this function is not called, the flags default to TRX_NEED_X. If the analysis module needs some other information (velocities, forces), it can call this function to load additional information from the trajectory.
void gmx::TrajectoryAnalysisSettings::setHelpText | ( | const ArrayRef< const char *const > & | help | ) |
Sets the help text for the module from string array.
[in] | help | String array to set as the description. |
std::bad_alloc | if out of memory. |
Formatting for the help text is described on Help formatting.
Example usage:
void gmx::TrajectoryAnalysisSettings::setPBC | ( | bool | bPBC | ) |
Sets whether PBC are used.
[in] | bPBC | true if PBC should be used. |
If called in TrajectoryAnalysisModule::initOptions(), this function sets the default for whether PBC are used in the analysis. If efNoUserPBC is not set, a command-line option is provided for the user to override the default value. If called later, it overrides the setting provided by the user or an earlier call.
If this function is not called, the default is to use PBC.
If PBC are not used, the pbc
pointer passed to TrajectoryAnalysisModule::analyzeFrame() is NULL. The value of the flag can also be accessed with hasPBC().
void gmx::TrajectoryAnalysisSettings::setRmPBC | ( | bool | bRmPBC | ) |
Sets whether molecules are made whole.
[in] | bRmPBC | true if molecules should be made whole. |
If called in TrajectoryAnalysisModule::initOptions(), this function sets the default for whether molecules are made whole. If efNoUserRmPBC is not set, a command-line option is provided for the user to override the default value. If called later, it overrides the setting provided by the user or an earlier call.
If this function is not called, the default is to make molecules whole.
The main use of this function is to call it with false
if your analysis program does not require whole molecules as this can increase the performance. In such a case, you can also specify efNoUserRmPBC to not to confuse the user with an option that would only slow the program down.