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37 * Implements gmx::analysismodules::Trajectory.
39 * \author Sergey Gorelov <gorelov_sv@pnpi.nrcki.ru>
40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
41 * \author Alexey Shvetsov <alexxyum@gmail.com>
42 * \ingroup module_trajectoryanalysis
46 #include "dssptools.h"
50 #include <iostream> //remove
52 #include <gromacs/trajectoryanalysis.h>
57 namespace analysismodules
60 class Dssp : public TrajectoryAnalysisModule
65 void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
67 void optionsFinished(TrajectoryAnalysisSettings* settings) override;
70 void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
72 void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* /* pdata */) override;
74 void finishAnalysis(int nframes) override;
75 void writeOutput() override;
78 initParameters initParams;
79 std::string filename_;
82 std::vector<std::pair<int, std::string>> data;
88 void Dssp::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
90 static const char* const desc[] = {
94 StringOption("o").store(&filename_).required().defaultValue("SSP.dat").description("Filename for DSSP output"));
95 options->addOption(RealOption("cutoff").store(&initParams.cutoff_).required().defaultValue(4.0).description(
96 "cutoff for neighbour search"));
98 SelectionOption("sel").store(&initParams.sel_).required().description(
101 EnumOption<NBSearchMethod>("algo").store(&initParams.NBS).required().defaultValue(NBSearchMethod::DSSP).enumValue(NBSearchMethodNames).description("Algorithm for search residues' neighbours"));
103 BooleanOption("addh").store(&initParams.addHydrogens).defaultValue(false).description("Add hydrogens or not"));
105 BooleanOption("p").store(&initParams.PPHelices).defaultValue(true).description("Prefer Pi Helices"));
107 BooleanOption("v").store(&initParams.verbose).defaultValue(false).description(">:("));
108 settings->setHelpText(desc);
112 void Dssp::optionsFinished(TrajectoryAnalysisSettings* /* settings */) {
116 void Dssp::initAnalysis(const TrajectoryAnalysisSettings &settings, const TopologyInformation& top)
118 DT.initAnalysis(top, initParams);
122 void Dssp::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* /* pdata*/)
124 DT.analyzeFrame(frnr, fr, pbc);
127 void Dssp::finishAnalysis(int /*nframes*/) {
133 void Dssp::writeOutput() {
135 std::ofstream dsspout;
136 dsspout.open(filename_, std::ofstream::out | std::ofstream::trunc);
137 dsspout << nres << "\n";
138 for (std::size_t i{ 0 }; i < data.size(); ++i)
140 for(std::size_t j{0}; j < data[i].second.size(); ++j){
141 dsspout << data[i].second[j];
149 const char DsspInfo::name[] = "dssp";
150 const char DsspInfo::shortDescription[] = "Calculate protein secondary structure via DSSP algo";
152 TrajectoryAnalysisModulePointer DsspInfo::create()
154 return TrajectoryAnalysisModulePointer(new Dssp);
157 } // namespace analysismodules
161 int main(int argc, char *argv[]) {
162 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<gmx::analysismodules::Dssp>(argc, argv);