src/gromacs/trajectoryanalysis/runnercommon.h

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  35 /*! \internal \file
  36  * \brief
  37  * Declares gmx::TrajectoryAnalysisRunnerCommon.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #ifndef GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
  43 #define GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
  44
  45 #include "gromacs/utility/classhelpers.h"
  46
  47 struct t_trxframe;
  48
  49 namespace gmx
  50 {
  51
  52 class Options;
  53 class SelectionCollection;
  54 class TopologyInformation;
  55 class TrajectoryAnalysisSettings;
  56
  57 /*! \internal
  58  * \brief
  59  * Implements common trajectory analysis runner functionality.
  60  *
  61  * As there is currently only one runner (TrajectoryAnalysisCommandLineRunner),
  62  * the division of responsibilities is not yet very clear.
  63  *
  64  * \ingroup module_trajectoryanalysis
  65  */
  66 class TrajectoryAnalysisRunnerCommon
  67 {
  68     public:
  69         /*! \brief
  70          * Initializes a new runner helper.
  71          *
  72          * \param    settings  Settings object to use.
  73          */
  74         explicit TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings *settings);
  75         ~TrajectoryAnalysisRunnerCommon();
  76
  77         /*! \brief
  78          * Initializes common options for trajectory analysis.
  79          *
  80          * \param[in,out] options  Options object to add the options to.
  81          */
  82         void initOptions(Options *options);
  83         //! Scales time option values according to the time unit set.
  84         void scaleTimeOptions(Options *options);
  85         /*! \brief
  86          * Processes common option values after they have been parsed.
  87          *
  88          * \param[in,out] options Options object in which options are stored.
  89          */
  90         void optionsFinished(Options *options);
  91         //! Initialize index groups for selections.
  92         void initIndexGroups(SelectionCollection *selections,
  93                              bool                 bUseDefaults);
  94         //! Free memory allocated for index groups.
  95         void doneIndexGroups(SelectionCollection *selections);
  96         //! Load topology information if provided and/or required.
  97         void initTopology(SelectionCollection *selections);
  98         /*! \brief
  99          * Reads the first frame from the trajectory.
 100          *
 101          * After this call, frame() returns the first frame.
 102          */
 103         void initFirstFrame();
 104         /*! \brief
 105          * Reads the next frame from the trajectory.
 106          *
 107          * \returns false if there were no more frames.
 108          *
 109          * After this call, frame() returns the newly loaded frame.
 110          */
 111         bool readNextFrame();
 112         /*! \brief
 113          * Performs common initialization for the currently loaded frame.
 114          *
 115          * Currently, makes molecules whole if requested.
 116          */
 117         void initFrame();
 118
 119         //! Returns true if input data comes from a trajectory.
 120         bool hasTrajectory() const;
 121         //! Returns the topology information object.
 122         const TopologyInformation &topologyInformation() const;
 123         //! Returns the currently loaded frame.
 124         t_trxframe                &frame() const;
 125
 126     private:
 127         class Impl;
 128
 129         PrivateImplPointer<Impl> impl_;
 130 };
 131
 132 } // namespace gmx
 133
 134 #endif