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/*! \internal \file
* \brief
* Declares trajectory analysis module for basic selection information.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
#ifndef GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
#define GMX_TRAJECTORYANALYSIS_MODULES_SELECT_H
-#include <string>
-#include <vector>
-
-#include "../analysismodule.h"
-#include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/analysisdata/modules/average.h"
-#include "gromacs/selection/selection.h"
+#include "gromacs/trajectoryanalysis/analysismodule.h"
namespace gmx
{
-class SelectionOptionInfo;
-
namespace analysismodules
{
-class Select : public TrajectoryAnalysisModule
+class SelectInfo
{
public:
static const char name[];
static const char shortDescription[];
-
- Select();
- virtual ~Select();
-
- virtual void initOptions(Options *options,
- TrajectoryAnalysisSettings *settings);
- virtual void optionsFinished(Options *options,
- TrajectoryAnalysisSettings *settings);
- virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
- const TopologyInformation &top);
-
- virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
- TrajectoryAnalysisModuleData *pdata);
-
- virtual void finishAnalysis(int nframes);
- virtual void writeOutput();
-
- private:
- SelectionList sel_;
- SelectionOptionInfo *selOpt_;
-
- std::string fnSize_;
- std::string fnFrac_;
- std::string fnIndex_;
- std::string fnNdx_;
- std::string fnMask_;
- std::string fnOccupancy_;
- std::string fnPDB_;
- bool bDump_;
- bool bTotNorm_;
- bool bFracNorm_;
- bool bResInd_;
- std::string resNumberType_;
- std::string pdbAtoms_;
-
- const TopologyInformation *top_;
- std::vector<int> totsize_;
- AnalysisData sdata_;
- AnalysisData cdata_;
- AnalysisData idata_;
- AnalysisData mdata_;
- AnalysisDataAverageModulePointer occupancyModule_;
+ static TrajectoryAnalysisModulePointer create();
};
} // namespace analysismodules
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff