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36 %PostInitialisationCode
43 #include <gromacs/fileio/trx.h>
44 #include "numpy_conv.h"
70 SIP_PYOBJECT x /NoSetter/ {
72 sipPy = array2dToNumpy(sipCpp->natoms, 3, sipCpp->x);
76 SIP_PYOBJECT v /NoSetter/ {
78 sipPy = array2dToNumpy(sipCpp->natoms, 3, sipCpp->v);
82 SIP_PYOBJECT f /NoSetter/ {
84 sipPy = array2dToNumpy(sipCpp->natoms, 3, sipCpp->f);
88 SIP_PYOBJECT box /NoSetter/ {
90 sipPy = array2dToNumpy(3, 3, sipCpp->box);
96 /*t_gmxvmdplugin* *vmdplugin; */
102 #include <gromacs/pbcutil/pbc.h>
103 #include "numpy_conv.h"
109 SIP_PYOBJECT box /NoSetter/ {
111 sipPy = array2dToNumpy(3, 3, sipCpp->box);
114 SIP_PYOBJECT fbox_diag /NoSetter/ {
116 sipPy = array1dToNumpy(3, sipCpp->fbox_diag);
119 SIP_PYOBJECT hbox_diag /NoSetter/ {
121 sipPy = array1dToNumpy(3, sipCpp->hbox_diag);
124 SIP_PYOBJECT mhbox_diag /NoSetter/ {
126 sipPy = array1dToNumpy(3, sipCpp->mhbox_diag);
131 double limit_distance2;
133 /*ivec tric_shift[MAX_NTRICVEC];*/
134 /*rvec tric_vec[MAX_NTRICVEC];*/
137 class TrajectoryAnalysisModuleData /NoDefaultCtors/ {
140 #include <gromacs/trajectoryanalysis/analysismodule.h>
145 virtual void finish() = 0;
149 #include "gromacs/utility/exceptions.h"
152 %VirtualErrorHandler vehandler
153 SIP_RELEASE_GIL(sipGILState);
155 GMX_THROW(gmx::InternalError("Python virtual overload raised an exception, see traceback"));
160 class TrajectoryAnalysisModule /VirtualErrorHandler=vehandler/ {
163 #include <gromacs/trajectoryanalysis/analysismodule.h>
167 virtual void initOptions(Options *options, TrajectoryAnalysisSettings *settings) = 0;
168 virtual void optionsFinished(Options *options, TrajectoryAnalysisSettings *settings);
169 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) = 0;
170 virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings, const t_trxframe &fr);
171 // virtual TrajectoryAnalysisModuleDataPointer startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections);
172 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, TrajectoryAnalysisModuleData *pdata) = 0;
173 virtual void finishFrames(TrajectoryAnalysisModuleData *pdata);
174 virtual void finishAnalysis(int nframes) = 0;
175 virtual void writeOutput() = 0;
176 virtual const std::vector<TrajectoryAnalysisModule*> getBatch();
177 virtual const std::vector<char*> getArgv(int);
178 const char* name() const;
179 const char* description() const;
180 int datasetCount() const;
181 // const std::vector<std::string> datasetNames() const;
182 AbstractAnalysisData& datasetFromIndex(int index) const;
183 AbstractAnalysisData& datasetFromName(const char *name) const;
185 TrajectoryAnalysisModule(const char *name, const char *description);
187 TrajectoryAnalysisModule(const TrajectoryAnalysisModule &other);
190 %Exception gmx::InconsistentInputError(SIP_Exception) {
193 #include <gromacs/utility/exceptions.h>
198 const char *detail = sipExceptionRef.what();
201 PyErr_SetString(sipException_gmx_InconsistentInputError, detail);