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 IOptionsContainer;
  53 class SelectionCollection;
  54 class TimeUnitBehavior;
  55 class TopologyInformation;
  56 class TrajectoryAnalysisSettings;
  57
  58 /*! \internal
  59  * \brief
  60  * Implements common trajectory analysis runner functionality.
  61  *
  62  * As there is currently only one runner (TrajectoryAnalysisCommandLineRunner),
  63  * the division of responsibilities is not yet very clear.
  64  *
  65  * \ingroup module_trajectoryanalysis
  66  */
  67 class TrajectoryAnalysisRunnerCommon
  68 {
  69     public:
  70         /*! \brief
  71          * Initializes a new runner helper.
  72          *
  73          * \param    settings  Settings object to use.
  74          */
  75         explicit TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings *settings);
  76         ~TrajectoryAnalysisRunnerCommon();
  77
  78         /*! \brief
  79          * Initializes common options for trajectory analysis.
  80          *
  81          * \param[in,out] options  Options object to add the options to.
  82          * \param[in,out] timeUnitBehavior  Time unit behavior to use for adding
  83          *    and handling the `-tu` option.
  84          */
  85         void initOptions(IOptionsContainer *options, TimeUnitBehavior *timeUnitBehavior);
  86         //! Processes common option values after they have been parsed.
  87         void optionsFinished();
  88         //! Initialize index groups for selections.
  89         void initIndexGroups(SelectionCollection *selections,
  90                              bool                 bUseDefaults);
  91         //! Free memory allocated for index groups.
  92         void doneIndexGroups(SelectionCollection *selections);
  93         //! Load topology information if provided and/or required.
  94         void initTopology(SelectionCollection *selections);
  95         /*! \brief
  96          * Reads the first frame from the trajectory.
  97          *
  98          * After this call, frame() returns the first frame.
  99          */
 100         void initFirstFrame();
 101         /*! \brief
 102          * Reads the next frame from the trajectory.
 103          *
 104          * \returns false if there were no more frames.
 105          *
 106          * After this call, frame() returns the newly loaded frame.
 107          */
 108         bool readNextFrame();
 109         /*! \brief
 110          * Performs common initialization for the currently loaded frame.
 111          *
 112          * Currently, makes molecules whole if requested.
 113          */
 114         void initFrame();
 115
 116         //! Returns true if input data comes from a trajectory.
 117         bool hasTrajectory() const;
 118         //! Returns the topology information object.
 119         const TopologyInformation &topologyInformation() const;
 120         //! Returns the currently loaded frame.
 121         t_trxframe                &frame() const;
 122
 123     private:
 124         class Impl;
 125
 126         PrivateImplPointer<Impl> impl_;
 127 };
 128
 129 } // namespace gmx
 130
 131 #endif