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37 * Declares gmx::TrajectoryAnalysisRunnerCommon.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
42 #ifndef GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
43 #define GMX_TRAJECTORYANALYSIS_RUNNERCOMMON_H
45 #include "../legacyheaders/types/simple.h"
46 #include "gromacs/fileio/trx.h"
48 #include "../utility/common.h"
54 class SelectionCollection;
55 class TopologyInformation;
56 class TrajectoryAnalysisSettings;
60 * Implements common trajectory analysis runner functionality.
62 * As there is currently only one runner (TrajectoryAnalysisCommandLineRunner),
63 * the division of responsibilities is not yet very clear.
65 * \ingroup module_trajectoryanalysis
67 class TrajectoryAnalysisRunnerCommon
71 * Initializes a new runner helper.
73 * \param settings Settings object to use.
75 explicit TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings *settings);
76 ~TrajectoryAnalysisRunnerCommon();
79 * Initializes common options for trajectory analysis.
81 * \param[in,out] options Options object to add the options to.
83 void initOptions(Options *options);
84 //! Scales time option values according to the time unit set.
85 void scaleTimeOptions(Options *options);
87 * Processes common option values after they have been parsed.
89 * \param[in,out] options Options object in which options are stored.
91 void optionsFinished(Options *options);
92 //! Initialize index groups for selections.
93 void initIndexGroups(SelectionCollection *selections,
95 //! Free memory allocated for index groups.
96 void doneIndexGroups(SelectionCollection *selections);
97 //! Load topology information if provided and/or required.
98 void initTopology(SelectionCollection *selections);
100 * Reads the first frame from the trajectory.
102 * After this call, frame() returns the first frame.
104 void initFirstFrame();
106 * Reads the next frame from the trajectory.
108 * \returns false if there were no more frames.
110 * After this call, frame() returns the newly loaded frame.
112 bool readNextFrame();
114 * Performs common initialization for the currently loaded frame.
116 * Currently, makes molecules whole if requested.
120 //! Returns true if input data comes from a trajectory.
121 bool hasTrajectory() const;
122 //! Returns the topology information object.
123 const TopologyInformation &topologyInformation() const;
124 //! Returns the currently loaded frame.
125 t_trxframe &frame() const;
130 PrivateImplPointer<Impl> impl_;