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37 * Implements gmx::analysismodules::Freevolume.
39 * \author Titov Anatoly <Wapuk-cobaka@yandex.ru>
40 * \ingroup module_trajectoryanalysis
43 #include <gromacs/trajectoryanalysis.h>
44 #include <gromacs/trajectoryanalysis/topologyinformation.h>
45 #include <gromacs/selection/nbsearch.h>
56 // структура углов для одной краски
57 struct colorLocalAngles {
58 gmx::RVec a1{0., 0., 0.}, a2{0., 0., 0.};
59 gmx::RVec b1{0., 0., 0.}, b2{0., 0., 0.};
60 gmx::RVec n1{0., 0., 0.}, n2{0., 0., 0.};
61 double a12 {0}, b12 {0}, n12 {0};
62 std::vector< double > betaAngles;
65 // функция парсинга одной строки
66 void parseBetaListDATLine(const std::string ¤tLine, std::vector< std::vector< unsigned int > > &localInputBL) {
67 size_t equalCount = 0;
68 std::vector< unsigned int > a;
70 for (size_t i = 0; i < currentLine.size(); ++i) {
71 if (currentLine[i] == '=') { // подсчитываем число "пустых" символов
75 for (size_t j = temp + 1; j < currentLine.size(); ++j) {
76 if (currentLine[j] == 'B' || currentLine[j] == 'E') {
81 localInputBL.push_back(a);
82 for (size_t j = i; j <= temp; ++j) {
83 localInputBL.back().push_back(j - equalCount);
91 // функция нахождения бета-листов в структуре по файлу ДССП
92 void betaListDigestion(const std::string &inputFile, std::vector< std::vector< std::vector< unsigned int > > > &inputBL) {
94 std::ifstream file(inputFile);
96 getline(file, line); // считываем число в первой строке - кол-во осмысленных элементов в строках - нам не нужно
98 if (line.size() > 3) {
100 inputBL.resize(inputBL.size() + 1);
101 parseBetaListDATLine(line, inputBL.back());
104 } while (line.size() > 3);
106 throw "DSSP DAT FILE IS EMPTY";
111 // функция выделения индексов для бэталистов
112 inline void aminoacidsIndexation(const std::vector< size_t > &inputIndex, const gmx::TopologyInformation &top, std::vector< std::vector< size_t > > &aminoacidsIndex) {
113 aminoacidsIndex.resize(0);
114 for (size_t i = 0; i < inputIndex.size(); ++i) {
115 aminoacidsIndex.resize(std::max(aminoacidsIndex.size(), static_cast< size_t >(top.atoms()->atom[inputIndex[i]].resind + 1)));
116 aminoacidsIndex[top.atoms()->atom[inputIndex[i]].resind].push_back(inputIndex[i]);
120 // функция поиска RVec в кадре по имени->индексу
121 gmx::RVec returnRVec(const std::vector< gmx::RVec > &frame, const std::vector< std::pair< std::string, size_t > > &colorsIndex, const std::string &toFind) {
122 for (auto &i : colorsIndex) {
123 if (i.first == toFind) {
124 return frame[i.second];
127 throw "WRONG COLOR ATOM NAME TO EVALUATE VECTORS";
130 // функция векторного произведения двух RVec'ов
131 inline void RVecVecMultiply(gmx::RVec &n, const gmx::RVec &a, const gmx::RVec &b) {
132 n[0] = a[1] * b[2] - a[2] * b[1];
133 n[1] = a[2] * b[0] - a[0] * b[2];
134 n[2] = a[0] * b[1] - a[2] * b[0];
137 // поиск угла между двумя RVec'ами
138 inline double RVecAngle(const gmx::RVec &a, const gmx::RVec &b) {
139 return std::acos((a[0] * b[0] + a[1] * b[1] + a[2] * b[2]) / (a.norm() * b.norm())) * 180.0 / 3.14159265;
142 // вычисление внутренних углов в краске
143 void colorsAnglesEvaluation(const std::vector< gmx::RVec > &frame, const std::vector< std::vector< std::pair< std::string, size_t > > > &colorsIndex,
144 std::vector< colorLocalAngles > &colorStruct) {
145 colorStruct.resize(colorsIndex.size());
146 #pragma omp parallel for ordered schedule(dynamic)
147 for (size_t i = 0; i < colorsIndex.size(); ++i) {
148 colorStruct[i].betaAngles.resize(0);
150 colorStruct[i].a1 = returnRVec(frame, colorsIndex[i], "CAF") - returnRVec(frame, colorsIndex[i], "CAJ") + returnRVec(frame, colorsIndex[i], "CAK") - returnRVec(frame, colorsIndex[i], "CAO");
151 colorStruct[i].a1 /= colorStruct[i].a1.norm();
152 colorStruct[i].b1 = returnRVec(frame, colorsIndex[i], "CAO") - returnRVec(frame, colorsIndex[i], "CAJ") + returnRVec(frame, colorsIndex[i], "CAM") - returnRVec(frame, colorsIndex[i], "CAH") + returnRVec(frame, colorsIndex[i], "CAK") - returnRVec(frame, colorsIndex[i], "CAF");
153 colorStruct[i].b1 /= colorStruct[i].b1.norm();
154 RVecVecMultiply(colorStruct[i].n1, colorStruct[i].a1, colorStruct[i].b1);
155 colorStruct[i].n1 /= colorStruct[i].n1.norm();
157 colorStruct[i].a2 = returnRVec(frame, colorsIndex[i], "CAB") - returnRVec(frame, colorsIndex[i], "CBQ") + returnRVec(frame, colorsIndex[i], "CBP") - returnRVec(frame, colorsIndex[i], "CBL");
158 colorStruct[i].a2 /= colorStruct[i].a2.norm();
159 colorStruct[i].b2 = returnRVec(frame, colorsIndex[i], "CBL") - returnRVec(frame, colorsIndex[i], "CBQ") + returnRVec(frame, colorsIndex[i], "CBN") - returnRVec(frame, colorsIndex[i], "CBS") + returnRVec(frame, colorsIndex[i], "CBP") - returnRVec(frame, colorsIndex[i], "CAB");
160 colorStruct[i].b2 /= colorStruct[i].b2.norm();
161 RVecVecMultiply(colorStruct[i].n2, colorStruct[i].a2, colorStruct[i].b2);
162 colorStruct[i].n2 *= -1; // для "сонаправленности" векторов нормали
163 colorStruct[i].n2 /= colorStruct[i].n2.norm();
164 colorStruct[i].a12 = RVecAngle(colorStruct[i].a1, colorStruct[i].a2);
165 colorStruct[i].b12 = RVecAngle(colorStruct[i].b1, colorStruct[i].b2);
166 colorStruct[i].n12 = RVecAngle(colorStruct[i].n1, colorStruct[i].n2);
171 // вычисление направляющего вектора в бэта-листе
172 inline void betaListsRVecsEvaluation(const std::vector< gmx::RVec > &frame, const std::vector< std::vector< unsigned int > > &inputBetaLists,
173 std::vector< gmx::RVec > &temp, const std::vector< size_t > &inputCA) {
176 for (const auto &i : inputBetaLists) {
177 tempA = frame[inputCA[i[i.size() - 1]]] + frame[inputCA[i[i.size() - 2]]] - frame[inputCA[i[1]]] - frame[inputCA[i[0]]];
178 tempA /= tempA.norm();
179 temp.push_back(tempA);
183 //// определение близко ли к белку находится краска
184 //bool isNearPeptide(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
185 // /*gmx::AnalysisNeighborhood &nbhood, */const std::vector< size_t > &inputIndex,
186 // const std::vector< std::pair< std::string, size_t > > &inputColor) {
187 // /*gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
188 // gmx::AnalysisNeighborhoodPair pair;*/
190 // for (size_t i = 0; i < inputColor.size(); ++i) {
191 // std::cout << inputColor[i].first << " " << i << " / " << inputColor.size() << std::endl;
192 // gmx::AnalysisNeighborhood nbhood;
193 // nbhood.setCutoff(0.8);
194 // gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
195 // gmx::AnalysisNeighborhoodPair pair;
196 // gmx::AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(inputFrame[inputColor[i].second].as_vec());
198 // while (pairSearch.findNextPair(&pair)) {
199 // std::cout << ++count1 << " ";
200 // for (size_t j = 0; j < inputIndex.size(); ++j) {
201 // if (pair.refIndex() == inputIndex[j]) {
206 // std::cout << inputColor[i].first << " atom done" << std::endl;
211 // определение близко ли к белку находится краска
212 bool isNearPeptide( const std::vector< gmx::RVec > &inputFrame, const std::vector< size_t > &inputIndex,
213 const std::vector< std::pair< std::string, size_t > > &inputColor, const double cutOff) {
214 for (size_t i {0}; i < inputColor.size(); ++i) {
215 for (size_t j {0}; j < inputIndex.size(); ++j) {
216 if ((inputFrame[inputIndex[j]] - inputFrame[inputColor[i].second]).norm() <= cutOff) {
224 // поиск ближайших к краске бэта-листов
225 //inline void searchNearBetaLists(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
226 // gmx::AnalysisNeighborhood &nbhood,
227 // const std::vector< std::vector< unsigned int > > &inputBLists,
228 // const std::vector< std::pair< std::string, size_t > > &inputColor,
229 // std::vector< bool > &outputList, const std::vector< std::vector< size_t > > &inputAminoacids) {
230 // outputList.resize(0);
231 // outputList.resize(inputBLists.size(), false);
232 // gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
233 // gmx::AnalysisNeighborhoodPair pair;
234 // for (const auto &i : inputColor) {
235 // while (nbsearch.startPairSearch(inputFrame[i.second].as_vec()).findNextPair(&pair)) {
236 // for (size_t j = 0; j < inputBLists.size(); ++j) {
237 // for (size_t k = 0; k < inputBLists[j].size(); ++k) {
238 // for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
239 // if (pair.testIndex() == inputAminoacids[inputBLists[j][k]][m]) {
240 // outputList[j] = true;
249 inline void searchNearBetaLists(const std::vector< gmx::RVec > &inputFrame, const std::vector< std::vector< unsigned int > > &inputBLists,
250 const std::vector< std::pair< std::string, size_t > > &inputColor, std::vector< bool > &outputList,
251 const std::vector< std::vector< size_t > > &inputAminoacids, const double cutOff) {
252 outputList.resize(0);
253 outputList.resize(inputBLists.size(), false);
254 //std::cout << inputColor.size() << " " << inputBLists.size() << " " << inputAminoacids.size() << "\n";
255 for (size_t i {0}; i < inputColor.size(); ++i) {
256 for (size_t j = 0; j < inputBLists.size(); ++j) {
257 for (size_t k = 0; k < inputBLists[j].size(); ++k) {
258 for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
259 std::cout << inputFrame[inputAminoacids[inputBLists[j][k]][m]][0] << " " << inputFrame[inputAminoacids[inputBLists[j][k]][m]][1] << " " <<
260 inputFrame[inputAminoacids[inputBLists[j][k]][m]][2] << "\n";
261 if ((inputFrame[inputAminoacids[inputBLists[j][k]][m]] - inputFrame[inputColor[i].second]).norm() <= cutOff) {
262 outputList[j] = true;
264 m = inputAminoacids[inputBLists[j][k]].size() + 1;
265 k = inputBLists[j].size() + 1;
273 // определение углов между краской и направляющим вектором бэта-листа
274 inline void computeAnglesColorsVsBeta(const gmx::RVec &inputBetaRVec, colorLocalAngles &colorFormation) {
275 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a1));
276 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b1));
277 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n1));
278 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a2));
279 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b2));
280 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n2));
283 // функция записи в файл значений углов для кадра
284 void anglesFileDump(const int frameNum, const std::string &output, const std::vector< bool > &toPeptide, const std::vector< colorLocalAngles > &colorFormation) {
285 std::ofstream file(output, std::ofstream::app);
287 std::vector< double > betaTemp;
289 file << "frame =" << std::setw(8) << frameNum << std::endl;
290 for (size_t i = 0; i < colorFormation.size(); ++i) {
291 file << "color #" << std::setw(3) << i;
293 file << std::setw(4) << "yes";
295 file << std::setw(4) << "no";
297 file << std::setw(7) << std::setprecision(2) << colorFormation[i].a12 << std::setw(7) << colorFormation[i].b12 << std::setw(7) << colorFormation[i].n12;
298 temp = colorFormation[i].betaAngles.size() / 6;
300 file << std::setw(4) << 0;
302 betaTemp.resize(6, 0.); // magic number, meh
303 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
304 betaTemp[j % 6] += colorFormation[i].betaAngles[j];
306 for (size_t j = 0; j < betaTemp.size(); ++j) {
309 file << std::setw(4) << temp;
310 for (size_t j = 0; j < betaTemp.size(); ++j) {
311 file << std::setw(7) << std::setprecision(2) << betaTemp[j];
313 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
314 file << std::setw(7) << std::setprecision(2) << colorFormation[i].betaAngles[j];
323 * \ingroup module_trajectoryanalysis
325 class colorVec : public gmx::TrajectoryAnalysisModule
332 //! Set the options and setting
333 virtual void initOptions(gmx::IOptionsContainer *options,
334 gmx::TrajectoryAnalysisSettings *settings);
336 //! First routine called by the analysis framework
337 // virtual void initAnalysis(const t_trxframe &fr, t_pbc *pbc);
338 virtual void initAnalysis(const gmx::TrajectoryAnalysisSettings &settings,
339 const gmx::TopologyInformation &top);
341 //! Call for each frame of the trajectory
342 // virtual void analyzeFrame(const t_trxframe &fr, t_pbc *pbc);
343 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
344 gmx::TrajectoryAnalysisModuleData *pdata);
346 //! Last routine called by the analysis framework
347 // virtual void finishAnalysis(t_pbc *pbc);
348 virtual void finishAnalysis(int nframes);
350 //! Routine to write output, that is additional over the built-in
351 virtual void writeOutput();
355 gmx::SelectionList sel_;
356 std::string fnOut {"name"}; // selectable
357 std::string fnBetaListsDat; // selectable
358 float effRad {0.8}; // selectable
359 std::vector< size_t > index;
360 std::vector< size_t > indexCA;
361 std::vector< std::vector< size_t > > aminoacidsIndex;
362 std::vector< std::vector< std::pair< std::string, size_t > > > colorsNames;
363 std::vector< std::vector< std::vector< unsigned int > > > betaLists;
364 gmx::AnalysisNeighborhood nb_;
366 // Copy and assign disallowed by base.
369 colorVec::colorVec(): TrajectoryAnalysisModule()
373 colorVec::~colorVec()
386 colorVec::initOptions( gmx::IOptionsContainer *options,
387 gmx::TrajectoryAnalysisSettings *settings)
389 static const char *const desc[] = {
390 "[THISMODULE] to be done"
392 // Add the descriptive text (program help text) to the options
393 settings->setHelpText(desc);
394 // Add option for selection list
395 options->addOption(gmx::SelectionOption("sel")
397 .required().dynamicMask().multiValue()
398 .description("select pepride and colors / -sf"));
399 // Add option for input file names
400 options->addOption(gmx::StringOption("dat")
401 .store(&fnBetaListsDat)
402 .description("a file to make dynamic beta lists"));
403 // Add option for output file name
404 options->addOption(gmx::StringOption("out")
406 .description("Index file for the algorithm output."));
407 // Add option for effRad constant
408 options->addOption(gmx::FloatOption("efRad")
410 .description("max distance from colors to peptide in nm to consider to be \"near\""));
411 // Control input settings
412 settings->setFlags(gmx::TrajectoryAnalysisSettings::efNoUserPBC);
413 settings->setFlag(gmx::TrajectoryAnalysisSettings::efUseTopX);
414 //settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
415 settings->setPBC(true);
419 colorVec::initAnalysis( const gmx::TrajectoryAnalysisSettings &settings,
420 const gmx::TopologyInformation &top)
422 // считывание индекса
424 for (gmx::ArrayRef< const int >::iterator ai {sel_.front().atomIndices().begin()}; (ai < sel_.front().atomIndices().end()); ai++) {
425 index.push_back(static_cast< size_t >(*ai));
427 // считывание индекса
429 for (gmx::ArrayRef< const int >::iterator ai {sel_[1].atomIndices().begin()}; (ai < sel_[2].atomIndices().end()); ai++) {
430 index.push_back(static_cast< size_t >(*ai));
433 colorsNames.resize(sel_.size() - 2);
434 for (size_t i = 2; i < sel_.size(); ++i) {
435 for (gmx::ArrayRef< const int >::iterator ai {sel_[i].atomIndices().begin()}; (ai < sel_[i].atomIndices().end()); ai++) {
436 colorsNames[i - 2].push_back(std::make_pair(*(top.atoms()->atomname[*ai]), static_cast< size_t >(*ai)));
439 // разбор dat файла для создания бэта листов
440 betaListDigestion(fnBetaListsDat, betaLists);
441 // разбор топологии для индексации бета листов
442 aminoacidsIndexation(index, top, aminoacidsIndex);
443 // задание радиуса рассматриваемых соседей
444 nb_.setCutoff(effRad);
446 * формально можно сделать:
447 * найти соотношение между именами для углов и индексными номерами
448 * заполнить std::vector< std::vector< size_t > > nameToIndex;
449 * и в последствии считать:
450 * a1 = frame[nameToIndex[0][1] + ... - ... - ...
451 * b1 a2 b2 по аналогии только для [@<-[1, 2, 3]]
457 colorVec::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, gmx::TrajectoryAnalysisModuleData *pdata)
459 std::vector< gmx::RVec > trajectoryFrame;
460 trajectoryFrame.resize(0);
461 // считывания текущего фрейма траектории
462 for (size_t i {0}; i < fr.natoms; ++i) {
463 trajectoryFrame.push_back(fr.x[i]);
465 // подсчёт углов в красках
466 std::vector< colorLocalAngles > colorFormation;
467 colorsAnglesEvaluation(trajectoryFrame, colorsNames, colorFormation);
468 // рассчёт положения относительно белка
470 * формально можно совместить определение близости с белком и определение ближайших бэта-листов
471 * для этого думаю нужно как-то соотнести или сделать соотношение между индексом и бэта-листами (т.е. хранить что бы за О(1) делать)
475 std::vector< bool > colorsToPeptide;
476 colorsToPeptide.resize(0);
477 colorsToPeptide.resize(colorsNames.size(), false);
478 for (size_t i = 0; i < colorsNames.size(); ++i) {
479 colorsToPeptide[i] = isNearPeptide(trajectoryFrame, index, colorsNames[i], effRad * 9000);
481 // расчёт угла и среднего угла с ближайшими бета листами
482 std::vector< std::vector< bool > > colorsToBeta;
483 colorsToBeta.resize(0);
484 colorsToBeta.resize(colorsNames.size());
485 std::vector< std::vector< double > > colorsToBetaAngles;
486 colorsToBetaAngles.resize(0);
487 std::vector< gmx::RVec > betaListsRVecs;
488 std::cout << "\n\nttest\n";
489 betaListsRVecsEvaluation(trajectoryFrame, betaLists[frnr], betaListsRVecs, indexCA);
490 for (size_t i = 0; i < colorsToPeptide.size(); ++i) {
491 if (colorsToPeptide[i]) {
492 searchNearBetaLists(trajectoryFrame, betaLists[frnr], colorsNames[i], colorsToBeta[i], aminoacidsIndex, effRad * 9000);
495 for (size_t i = 0; i < colorsToBeta.size(); ++i) {
496 for (size_t j = 0; j < colorsToBeta[i].size(); ++j) {
497 if (colorsToBeta[i][j]) {
498 computeAnglesColorsVsBeta(betaListsRVecs[j], colorFormation[i]);
502 // вывод в файл(ы) информацию для фрейма
503 anglesFileDump(frnr, fnOut, colorsToPeptide, colorFormation);
507 colorVec::finishAnalysis(int nframes)
513 colorVec::writeOutput()
517 * frame #<current frame number>
518 * color #<color number> <yes/no for "close" to peptide> a12 b12 n12 <number of beta lists> <6 avg beta angles> [<6 angles for each beta list>]
524 * The main function for the analysis template.
527 main(int argc, char *argv[])
529 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<colorVec>(argc, argv);