/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010-2018, The GROMACS development team.
+ * Copyright (c) 2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-template <typename T> class ArrayRef;
+template<typename T>
+class ArrayRef;
class AnalysisDataPlotSettings;
class ICommandLineOptionsModuleSettings;
*/
class TrajectoryAnalysisSettings
{
- public:
- //! Recognized flags.
- enum
- {
- /*! \brief
- * 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.
- */
- efRequireTop = 1<<0,
- /*! \brief
- * Requests topology coordinates.
- *
- * If this flag is specified, the position coordinates loaded from the
- * topology can be accessed, otherwise they are not loaded.
- *
- * \see TopologyInformation
- */
- efUseTopX = 1<<1,
- /*! \brief
- * Requests topology coordinates.
- *
- * If this flag is specified, the velocity coordinates loaded from the
- * topology can be accessed, otherwise they are not loaded.
- *
- * \see TopologyInformation
- */
- efUseTopV = 1<<2,
- /*! \brief
- * 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.
- *
- * \see setPBC()
- */
- efNoUserPBC = 1<<4,
- /*! \brief
- * Disallows the user from changing PBC removal.
- *
- * \see setRmPBC()
- */
- efNoUserRmPBC = 1<<5,
- };
-
- //! Initializes default settings.
- TrajectoryAnalysisSettings();
- ~TrajectoryAnalysisSettings();
-
- //! Injects command line options module settings for some methods to use.
- void setOptionsModuleSettings(ICommandLineOptionsModuleSettings *settings);
-
- //! Returns the time unit the user has requested.
- TimeUnit timeUnit() const;
- //! Returns common settings for analysis data plot modules.
- const AnalysisDataPlotSettings &plotSettings() const;
-
- //! Returns the currently set flags.
- unsigned long flags() const;
- //! Tests whether a flag has been set.
- bool hasFlag(unsigned long flag) const;
+public:
+ //! Recognized flags.
+ enum
+ {
/*! \brief
- * Returns whether PBC should be used.
+ * Forces loading of a topology file.
*
- * 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().
+ * If this flag is not specified, the topology file is loaded only
+ * if it is provided on the command line explicitly.
*/
- bool hasPBC() const;
+ efRequireTop = 1 << 0,
/*! \brief
- * Returns whether molecules should be made whole.
+ * Requests topology coordinates.
*
- * See hasPBC() for information on accessing or overriding the
- * user-provided value.
- */
- bool hasRmPBC() const;
- //! Returns the currently set frame flags.
- int frflags() const;
-
- /*! \brief
- * Sets flags.
+ * If this flag is specified, the position coordinates loaded from the
+ * topology can be accessed, otherwise they are not loaded.
*
- * Overrides any earlier set flags.
- * By default, no flags are set.
+ * \see TopologyInformation
*/
- void setFlags(unsigned long flags);
- //! Sets or clears an individual flag.
- void setFlag(unsigned long flag, bool bSet = true);
+ efUseTopX = 1 << 1,
/*! \brief
- * Sets whether PBC are used.
- *
- * \param[in] bPBC true if PBC should be used.
+ * Requests topology coordinates.
*
- * If called in TrajectoryAnalysisModule::initOptions(), this function
- * sets the default for whether PBC are used in the analysis.
- * If \ref 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 flag is specified, the velocity coordinates loaded from the
+ * topology can be accessed, otherwise they are not loaded.
*
- * If this function is not called, the default is to use PBC.
- *
- * If PBC are not used, the \p pbc pointer passed to
- * TrajectoryAnalysisModule::analyzeFrame() is NULL.
- * The value of the flag can also be accessed with hasPBC().
- *
- * \see efNoUserPBC
+ * \see TopologyInformation
*/
- void setPBC(bool bPBC);
+ efUseTopV = 1 << 2,
/*! \brief
- * Sets whether molecules are made whole.
- *
- * \param[in] bRmPBC true if molecules should be made whole.
+ * Disallows the user from changing PBC handling.
*
- * If called in TrajectoryAnalysisModule::initOptions(), this function
- * sets the default for whether molecules are made whole.
- * If \ref 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 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.
*
- * If this function is not called, the default is to make molecules
- * whole.
- *
- * The main use of this function is to call it with \c false if your
- * analysis program does not require whole molecules as this can
- * increase the performance.
- * In such a case, you can also specify \ref efNoUserRmPBC to not to
- * confuse the user with an option that would only slow the program
- * down.
- *
- * \see efNoUserRmPBC
+ * \see setPBC()
*/
- void setRmPBC(bool bRmPBC);
+ efNoUserPBC = 1 << 4,
/*! \brief
- * Sets flags that determine what to read from the trajectory.
+ * Disallows the user from changing PBC removal.
*
- * \param[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.
+ * \see setRmPBC()
*/
- void setFrameFlags(int frflags);
-
- //! \copydoc ICommandLineOptionsModuleSettings::setHelpText()
- void setHelpText(const ArrayRef<const char *const> &help);
-
- private:
- class Impl;
-
- PrivateImplPointer<Impl> impl_;
-
- friend class TrajectoryAnalysisRunnerCommon;
+ efNoUserRmPBC = 1 << 5,
+ };
+
+ //! Initializes default settings.
+ TrajectoryAnalysisSettings();
+ ~TrajectoryAnalysisSettings();
+
+ //! Injects command line options module settings for some methods to use.
+ void setOptionsModuleSettings(ICommandLineOptionsModuleSettings* settings);
+
+ //! Returns the time unit the user has requested.
+ TimeUnit timeUnit() const;
+ //! Returns common settings for analysis data plot modules.
+ const AnalysisDataPlotSettings& plotSettings() const;
+
+ //! Returns the currently set flags.
+ unsigned long flags() const;
+ //! Tests whether a flag has been set.
+ bool hasFlag(unsigned long flag) const;
+ /*! \brief
+ * 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 hasPBC() const;
+ /*! \brief
+ * Returns whether molecules should be made whole.
+ *
+ * See hasPBC() for information on accessing or overriding the
+ * user-provided value.
+ */
+ bool hasRmPBC() const;
+ //! Returns the currently set frame flags.
+ int frflags() const;
+
+ /*! \brief
+ * Sets flags.
+ *
+ * Overrides any earlier set flags.
+ * By default, no flags are set.
+ */
+ void setFlags(unsigned long flags);
+ //! Sets or clears an individual flag.
+ void setFlag(unsigned long flag, bool bSet = true);
+ /*! \brief
+ * Sets whether PBC are used.
+ *
+ * \param[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 \ref 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 \p pbc pointer passed to
+ * TrajectoryAnalysisModule::analyzeFrame() is NULL.
+ * The value of the flag can also be accessed with hasPBC().
+ *
+ * \see efNoUserPBC
+ */
+ void setPBC(bool bPBC);
+ /*! \brief
+ * Sets whether molecules are made whole.
+ *
+ * \param[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 \ref 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 \c false if your
+ * analysis program does not require whole molecules as this can
+ * increase the performance.
+ * In such a case, you can also specify \ref efNoUserRmPBC to not to
+ * confuse the user with an option that would only slow the program
+ * down.
+ *
+ * \see efNoUserRmPBC
+ */
+ void setRmPBC(bool bRmPBC);
+ /*! \brief
+ * Sets flags that determine what to read from the trajectory.
+ *
+ * \param[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 setFrameFlags(int frflags);
+
+ //! \copydoc ICommandLineOptionsModuleSettings::setHelpText()
+ void setHelpText(const ArrayRef<const char* const>& help);
+
+private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+
+ friend class TrajectoryAnalysisRunnerCommon;
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff