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 ITopologyProvider;
  54 class SelectionCollection;
  55 class TimeUnitBehavior;
  56 class TopologyInformation;
  57 class TrajectoryAnalysisSettings;
  58
  59 /*! \internal
  60  * \brief
  61  * Implements common trajectory analysis runner functionality.
  62  *
  63  * As there is currently only one runner (TrajectoryAnalysisCommandLineRunner),
  64  * the division of responsibilities is not yet very clear.
  65  *
  66  * \ingroup module_trajectoryanalysis
  67  */
  68 class TrajectoryAnalysisRunnerCommon
  69 {
  70     public:
  71         /*! \brief
  72          * Initializes a new runner helper.
  73          *
  74          * \param    settings  Settings object to use.
  75          */
  76         explicit TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings *settings);
  77         ~TrajectoryAnalysisRunnerCommon();
  78
  79         //! Returns a topology provider for SelectionOptionBehavior.
  80         ITopologyProvider *topologyProvider();
  81
  82         /*! \brief
  83          * Initializes common options for trajectory analysis.
  84          *
  85          * \param[in,out] options  Options object to add the options to.
  86          * \param[in,out] timeUnitBehavior  Time unit behavior to use for adding
  87          *    and handling the `-tu` option.
  88          */
  89         void initOptions(IOptionsContainer *options, TimeUnitBehavior *timeUnitBehavior);
  90         //! Processes common option values after they have been parsed.
  91         void optionsFinished();
  92         //! Load topology information if provided and/or required.
  93         void initTopology();
  94         /*! \brief
  95          * Reads the first frame from the trajectory.
  96          *
  97          * After this call, frame() returns the first frame.
  98          */
  99         void initFirstFrame();
 100         /*! \brief
 101          * Initializes the index in frame() that specifies the atoms contained.
 102          *
 103          * Can be called after selections have been compiled.
 104          */
 105         void initFrameIndexGroup();
 106         /*! \brief
 107          * Reads the next frame from the trajectory.
 108          *
 109          * \returns false if there were no more frames.
 110          *
 111          * After this call, frame() returns the newly loaded frame.
 112          */
 113         bool readNextFrame();
 114         /*! \brief
 115          * Performs common initialization for the currently loaded frame.
 116          *
 117          * Currently, makes molecules whole if requested.
 118          */
 119         void initFrame();
 120
 121         //! Returns true if input data comes from a trajectory.
 122         bool hasTrajectory() const;
 123         //! Returns the topology information object.
 124         const TopologyInformation &topologyInformation() const;
 125         //! Returns the currently loaded frame.
 126         t_trxframe                &frame() const;
 127
 128     private:
 129         class Impl;
 130
 131         PrivateImplPointer<Impl> impl_;
 132 };
 133
 134 } // namespace gmx
 135
 136 #endif