src/gromacs/trajectoryanalysis/runnercommon.h

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  36 /*! \internal \file
  37  * \brief
  38  * Declares gmx::TrajectoryAnalysisRunnerCommon.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \ingroup module_trajectoryanalysis
  42  */
  43 #ifndef GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
  44 #define GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
  45
  46 #include "gromacs/utility/classhelpers.h"
  47
  48 struct t_trxframe;
  49
  50 namespace gmx
  51 {
  52
  53 class IOptionsContainer;
  54 class ITopologyProvider;
  55 class SelectionCollection;
  56 class TimeUnitBehavior;
  57 class TopologyInformation;
  58 class TrajectoryAnalysisSettings;
  59
  60 /*! \internal
  61  * \brief
  62  * Implements common trajectory analysis runner functionality.
  63  *
  64  * As there is currently only one runner (TrajectoryAnalysisCommandLineRunner),
  65  * the division of responsibilities is not yet very clear.
  66  *
  67  * \ingroup module_trajectoryanalysis
  68  */
  69 class TrajectoryAnalysisRunnerCommon
  70 {
  71 public:
  72     /*! \brief
  73      * Initializes a new runner helper.
  74      *
  75      * \param    settings  Settings object to use.
  76      */
  77     explicit TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings* settings);
  78     ~TrajectoryAnalysisRunnerCommon();
  79
  80     //! Returns a topology provider for SelectionOptionBehavior.
  81     ITopologyProvider* topologyProvider();
  82
  83     /*! \brief
  84      * Initializes common options for trajectory analysis.
  85      *
  86      * \param[in,out] options  Options object to add the options to.
  87      * \param[in,out] timeUnitBehavior  Time unit behavior to use for adding
  88      *    and handling the `-tu` option.
  89      */
  90     void initOptions(IOptionsContainer* options, TimeUnitBehavior* timeUnitBehavior);
  91     //! Processes common option values after they have been parsed.
  92     void optionsFinished();
  93     //! Load topology information if provided and/or required.
  94     void initTopology();
  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      * Initializes the index in frame() that specifies the atoms contained.
 103      *
 104      * Can be called after selections have been compiled.
 105      */
 106     void initFrameIndexGroup();
 107     /*! \brief
 108      * Reads the next frame from the trajectory.
 109      *
 110      * \returns false if there were no more frames.
 111      *
 112      * After this call, frame() returns the newly loaded frame.
 113      */
 114     bool readNextFrame();
 115     /*! \brief
 116      * Performs common initialization for the currently loaded frame.
 117      *
 118      * Currently, makes molecules whole if requested.
 119      */
 120     void initFrame();
 121
 122     //! Returns true if input data comes from a trajectory.
 123     bool hasTrajectory() const;
 124     //! Returns the topology information object.
 125     const TopologyInformation& topologyInformation() const;
 126     //! Returns the currently loaded frame.
 127     t_trxframe& frame() const;
 128
 129 private:
 130     class Impl;
 131
 132     PrivateImplPointer<Impl> impl_;
 133 };
 134
 135 } // namespace gmx
 136
 137 #endif