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37 * Declares trajectory analysis module for basic selection information.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
42 #ifndef GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
43 #define GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
48 #include "../analysismodule.h"
49 #include "gromacs/analysisdata/analysisdata.h"
50 #include "gromacs/analysisdata/modules/average.h"
51 #include "gromacs/selection/selection.h"
56 class SelectionOptionInfo;
58 namespace analysismodules
61 class Select : public TrajectoryAnalysisModule
64 static const char name[];
65 static const char shortDescription[];
70 virtual void initOptions(Options *options,
71 TrajectoryAnalysisSettings *settings);
72 virtual void optionsFinished(Options *options,
73 TrajectoryAnalysisSettings *settings);
74 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
75 const TopologyInformation &top);
77 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
78 TrajectoryAnalysisModuleData *pdata);
80 virtual void finishAnalysis(int nframes);
81 virtual void writeOutput();
85 SelectionOptionInfo *selOpt_;
92 std::string fnOccupancy_;
98 std::string resNumberType_;
99 std::string pdbAtoms_;
101 const TopologyInformation *top_;
102 std::vector<int> totsize_;
107 AnalysisDataAverageModulePointer occupancyModule_;
110 } // namespace analysismodules