share/template/template.cpp

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  35 #include <string>
  36 #include <vector>
  37
  38 #include <gromacs/trajectoryanalysis.h>
  39
  40 using namespace gmx;
  41
  42 /*! \brief
  43  * Template class to serve as a basis for user analysis tools.
  44  */
  45 class AnalysisTemplate : public TrajectoryAnalysisModule
  46 {
  47     public:
  48         AnalysisTemplate();
  49
  50         virtual void initOptions(IOptionsContainer          *options,
  51                                  TrajectoryAnalysisSettings *settings);
  52         virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
  53                                   const TopologyInformation        &top);
  54
  55         virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
  56                                   TrajectoryAnalysisModuleData *pdata);
  57
  58         virtual void finishAnalysis(int nframes);
  59         virtual void writeOutput();
  60
  61     private:
  62         class ModuleData;
  63
  64         std::string                      fnDist_;
  65         double                           cutoff_;
  66         Selection                        refsel_;
  67         SelectionList                    sel_;
  68
  69         AnalysisNeighborhood             nb_;
  70
  71         AnalysisData                     data_;
  72         AnalysisDataAverageModulePointer avem_;
  73 };
  74
  75
  76 AnalysisTemplate::AnalysisTemplate()
  77     : cutoff_(0.0)
  78 {
  79     registerAnalysisDataset(&data_, "avedist");
  80 }
  81
  82
  83 void
  84 AnalysisTemplate::initOptions(IOptionsContainer          *options,
  85                               TrajectoryAnalysisSettings *settings)
  86 {
  87     static const char *const desc[] = {
  88         "This is a template for writing your own analysis tools for",
  89         "GROMACS. The advantage of using GROMACS for this is that you",
  90         "have access to all information in the topology, and your",
  91         "program will be able to handle all types of coordinates and",
  92         "trajectory files supported by GROMACS. In addition,",
  93         "you get a lot of functionality for free from the trajectory",
  94         "analysis library, including support for flexible dynamic",
  95         "selections. Go ahead an try it![PAR]",
  96         "To get started with implementing your own analysis program,",
  97         "follow the instructions in the README file provided.",
  98         "This template implements a simple analysis programs that calculates",
  99         "average distances from a reference group to one or more",
 100         "analysis groups."
 101     };
 102
 103     settings->setHelpText(desc);
 104
 105     options->addOption(FileNameOption("o")
 106                            .filetype(eftPlot).outputFile()
 107                            .store(&fnDist_).defaultBasename("avedist")
 108                            .description("Average distances from reference group"));
 109
 110     options->addOption(SelectionOption("reference")
 111                            .store(&refsel_).required()
 112                            .description("Reference group to calculate distances from"));
 113     options->addOption(SelectionOption("select")
 114                            .storeVector(&sel_).required().multiValue()
 115                            .description("Groups to calculate distances to"));
 116
 117     options->addOption(DoubleOption("cutoff").store(&cutoff_)
 118                            .description("Cutoff for distance calculation (0 = no cutoff)"));
 119
 120     settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
 121 }
 122
 123
 124 void
 125 AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings &settings,
 126                                const TopologyInformation         & /*top*/)
 127 {
 128     nb_.setCutoff(static_cast<real>(cutoff_));
 129
 130     data_.setColumnCount(0, sel_.size());
 131
 132     avem_.reset(new AnalysisDataAverageModule());
 133     data_.addModule(avem_);
 134
 135     if (!fnDist_.empty())
 136     {
 137         AnalysisDataPlotModulePointer plotm(
 138                 new AnalysisDataPlotModule(settings.plotSettings()));
 139         plotm->setFileName(fnDist_);
 140         plotm->setTitle("Average distance");
 141         plotm->setXAxisIsTime();
 142         plotm->setYLabel("Distance (nm)");
 143         data_.addModule(plotm);
 144     }
 145 }
 146
 147
 148 void
 149 AnalysisTemplate::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
 150                                TrajectoryAnalysisModuleData *pdata)
 151 {
 152     AnalysisDataHandle         dh     = pdata->dataHandle(data_);
 153     const Selection           &refsel = pdata->parallelSelection(refsel_);
 154
 155     AnalysisNeighborhoodSearch nbsearch = nb_.initSearch(pbc, refsel);
 156     dh.startFrame(frnr, fr.time);
 157     for (size_t g = 0; g < sel_.size(); ++g)
 158     {
 159         const Selection &sel   = pdata->parallelSelection(sel_[g]);
 160         int              nr    = sel.posCount();
 161         real             frave = 0.0;
 162         for (int i = 0; i < nr; ++i)
 163         {
 164             SelectionPosition p = sel.position(i);
 165             frave += nbsearch.minimumDistance(p.x());
 166         }
 167         frave /= nr;
 168         dh.setPoint(g, frave);
 169     }
 170     dh.finishFrame();
 171 }
 172
 173
 174 void
 175 AnalysisTemplate::finishAnalysis(int /*nframes*/)
 176 {
 177 }
 178
 179
 180 void
 181 AnalysisTemplate::writeOutput()
 182 {
 183     // We print out the average of the mean distances for each group.
 184     for (size_t g = 0; g < sel_.size(); ++g)
 185     {
 186         fprintf(stderr, "Average mean distance for '%s': %.3f nm\n",
 187                 sel_[g].name(), avem_->average(0, g));
 188     }
 189 }
 190
 191 /*! \brief
 192  * The main function for the analysis template.
 193  */
 194 int
 195 main(int argc, char *argv[])
 196 {
 197     return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<AnalysisTemplate>(argc, argv);
 198 }