src/gromacs/trajectoryanalysis/tests/test_selection.cpp

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  36 /*! \internal \file
  37  * \brief Testing/debugging tool for the selection engine.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/options/basicoptions.h"
  45 #include "gromacs/options/ioptionscontainer.h"
  46 #include "gromacs/selection/selection.h"
  47 #include "gromacs/selection/selectionoption.h"
  48 #include "gromacs/trajectoryanalysis/analysismodule.h"
  49 #include "gromacs/trajectoryanalysis/analysissettings.h"
  50 #include "gromacs/trajectoryanalysis/cmdlinerunner.h"
  51 #include "gromacs/utility/arrayref.h"
  52 #include "gromacs/utility/exceptions.h"
  53
  54 namespace gmx
  55 {
  56
  57 class SelectionTester : public TrajectoryAnalysisModule
  58 {
  59 public:
  60     SelectionTester();
  61     ~SelectionTester() override;
  62
  63     void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
  64     void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
  65
  66     void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata) override;
  67
  68     void finishAnalysis(int nframes) override;
  69     void writeOutput() override;
  70
  71 private:
  72     void printSelections();
  73
  74     SelectionList selections_;
  75     int           nmaxind_;
  76 };
  77
  78 SelectionTester::SelectionTester() : nmaxind_(20) {}
  79
  80 SelectionTester::~SelectionTester() {}
  81
  82 void SelectionTester::printSelections()
  83 {
  84     fprintf(stderr, "\nSelections:\n");
  85     for (size_t g = 0; g < selections_.size(); ++g)
  86     {
  87         selections_[g].printDebugInfo(stderr, nmaxind_);
  88     }
  89     fprintf(stderr, "\n");
  90 }
  91
  92 void SelectionTester::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
  93 {
  94     static const char* const desc[] = { "This is a test program for selections." };
  95
  96     settings->setHelpText(desc);
  97
  98     options->addOption(
  99             SelectionOption("select").storeVector(&selections_).required().multiValue().description("Selections to test"));
 100     options->addOption(IntegerOption("pmax").store(&nmaxind_).description(
 101             "Maximum number of indices to print in lists (-1 = print all)"));
 102 }
 103
 104 void SelectionTester::initAnalysis(const TrajectoryAnalysisSettings& /*settings*/,
 105                                    const TopologyInformation& /*top*/)
 106 {
 107     printSelections();
 108 }
 109
 110 void SelectionTester::analyzeFrame(int /*frnr*/,
 111                                    const t_trxframe& /*fr*/,
 112                                    t_pbc* /*pbc*/,
 113                                    TrajectoryAnalysisModuleData* /*pdata*/)
 114 {
 115     fprintf(stderr, "\n");
 116     for (size_t g = 0; g < selections_.size(); ++g)
 117     {
 118         const Selection& sel = selections_[g];
 119         int              n;
 120
 121         fprintf(stderr, "  Atoms (%d pcs):", sel.atomCount());
 122         n = sel.atomCount();
 123         if (nmaxind_ >= 0 && n > nmaxind_)
 124         {
 125             n = nmaxind_;
 126         }
 127         ArrayRef<const int> atoms = sel.atomIndices();
 128         for (int i = 0; i < n; ++i)
 129         {
 130             fprintf(stderr, " %d", atoms[i] + 1);
 131         }
 132         if (n < sel.atomCount())
 133         {
 134             fprintf(stderr, " ...");
 135         }
 136         fprintf(stderr, "\n");
 137
 138         fprintf(stderr, "  Positions (%d pcs):\n", sel.posCount());
 139         n = sel.posCount();
 140         if (nmaxind_ >= 0 && n > nmaxind_)
 141         {
 142             n = nmaxind_;
 143         }
 144         for (int i = 0; i < n; ++i)
 145         {
 146             const SelectionPosition& p = sel.position(i);
 147             fprintf(stderr, "    (%.2f,%.2f,%.2f) r=%d, m=%d, n=%d\n", p.x()[XX], p.x()[YY],
 148                     p.x()[ZZ], p.refId(), p.mappedId(), p.atomCount());
 149         }
 150         if (n < sel.posCount())
 151         {
 152             fprintf(stderr, "    ...\n");
 153         }
 154     }
 155     fprintf(stderr, "\n");
 156 }
 157
 158 void SelectionTester::finishAnalysis(int /*nframes*/)
 159 {
 160     printSelections();
 161 }
 162
 163 void SelectionTester::writeOutput() {}
 164
 165 } // namespace gmx
 166
 167 /*! \internal \brief
 168  * The main function for the selection testing tool.
 169  */
 170 int main(int argc, char* argv[])
 171 {
 172     return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<gmx::SelectionTester>(argc, argv);
 173 }