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36 %PostInitialisationCode
43 #include <gromacs/fileio/trx.h>
44 #include "numpy_conv.h"
72 sipPy = array2dToNumpy(sipCpp->natoms, 3, sipCpp->x);
81 sipPy = array2dToNumpy(sipCpp->natoms, 3, sipCpp->v);
90 sipPy = array2dToNumpy(sipCpp->natoms, 3, sipCpp->f);
99 sipPy = array2dToNumpy(3, 3, sipCpp->box);
108 /*t_gmxvmdplugin* *vmdplugin; */
114 #include <gromacs/pbcutil/pbc.h>
115 #include "numpy_conv.h"
123 sipPy = array2dToNumpy(3, 3, sipCpp->box);
129 SIP_PYOBJECT fbox_diag {
131 sipPy = array1dToNumpy(3, sipCpp->fbox_diag);
137 SIP_PYOBJECT hbox_diag {
139 sipPy = array1dToNumpy(3, sipCpp->hbox_diag);
145 SIP_PYOBJECT mhbox_diag {
147 sipPy = array1dToNumpy(3, sipCpp->mhbox_diag);
155 double limit_distance2;
157 /*ivec tric_shift[MAX_NTRICVEC];*/
158 /*rvec tric_vec[MAX_NTRICVEC];*/
161 class TrajectoryAnalysisModuleData /NoDefaultCtors/ {
164 #include <gromacs/trajectoryanalysis/analysismodule.h>
169 virtual void finish() = 0;
173 #include "gromacs/utility/exceptions.h"
176 %VirtualErrorHandler vehandler
177 SIP_RELEASE_GIL(sipGILState);
179 GMX_THROW(gmx::InternalError("Python virtual overload raised an exception, see traceback"));
182 class TrajectoryAnalysisModule /VirtualErrorHandler=vehandler/ {
185 #include <gromacs/trajectoryanalysis/analysismodule.h>
189 virtual void initOptions(Options *options, TrajectoryAnalysisSettings *settings) = 0;
190 virtual void optionsFinished(Options *options, TrajectoryAnalysisSettings *settings);
191 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings, const TopologyInformation &top) = 0;
192 virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings, const t_trxframe &fr);
193 // virtual TrajectoryAnalysisModuleDataPointer startFrames (const AnalysisDataParallelOptions &opt, const SelectionCollection &selections);
194 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, TrajectoryAnalysisModuleData *pdata ) = 0;
195 virtual void finishFrames(TrajectoryAnalysisModuleData *pdata);
196 virtual void finishAnalysis(int nframes) = 0;
197 virtual void writeOutput() = 0;
198 const char* name() const;
199 const char* description() const;
200 int datasetCount() const;
202 TrajectoryAnalysisModule(const char *name, const char *description);
204 TrajectoryAnalysisModule(const TrajectoryAnalysisModule &other);
207 %Exception gmx::InconsistentInputError(SIP_Exception) {
210 #include <gromacs/utility/exceptions.h>
215 const char *detail = sipExceptionRef.what();
218 PyErr_SetString(sipException_gmx_InconsistentInputError, detail);