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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 {
62 std::vector< double > betaAngles;
65 // хрен пойми почему, но захотелось рекурсивно сделать | можно сделать и через вайл
66 long long returnBetaEnd(const std::string ¤tLine, long long pos) {
67 switch (currentLine[pos]) {
69 returnBetaEnd(currentLine, pos + 1);
72 returnBetaEnd(currentLine, pos + 1);
78 return (pos - 1); // формально логически лишняя строчка, но Qt ругается
81 // функция парсинга одной строки
82 void parseBetaListDATLine(const std::string ¤tLine, std::vector< std::vector< unsigned int > > &localInputBL) {
83 size_t equalCount = 0;
84 std::vector< unsigned int > a;
86 for (size_t i = 0; i < currentLine.size(); ++i) {
87 if (currentLine[i] == '=') { // подсчитываем число "пустых" символов
90 long long temp = returnBetaEnd(currentLine, i);
91 if (temp - static_cast< long long >(i) > 3) {
92 localInputBL.push_back(a);
93 for (size_t j = i; j <= temp; ++j) {
94 localInputBL.back().push_back(j - equalCount);
102 // функция нахождения бета-листов в структуре по файлу ДССП
103 void betaListDigestion(const std::string &inputFile, std::vector< std::vector< std::vector< unsigned int > > > &inputBL) {
105 std::ifstream file(inputFile);
107 getline(file, line); // считываем число в первой строке - кол-во осмысленных элементов в строках - нам не нужно
109 if (line.size() > 3) {
111 inputBL.resize(inputBL.size() + 1);
112 parseBetaListDATLine(line, inputBL.back());
115 } while (line.size() > 3);
117 throw "DSSP DAT FILE IS EMPTY";
122 // функция выделения индексов для бэталистов
123 inline void aminoacidsIndexation(const std::vector< size_t > &inputIndex, const gmx::TopologyInformation &top, std::vector< std::vector< size_t > > &aminoacidsIndex) {
124 aminoacidsIndex.resize(0);
125 for (size_t i = 0; i < inputIndex.size(); ++i) {
126 aminoacidsIndex.resize(std::max(aminoacidsIndex.size(), static_cast< size_t >(top.atoms()->atom[inputIndex[i]].resind + 1)));
127 aminoacidsIndex[top.atoms()->atom[inputIndex[i]].resind].push_back(inputIndex[i]);
131 // функция поиска RVec в кадре по имени->индексу
132 gmx::RVec returnRVec(const std::vector< gmx::RVec > &frame, const std::vector< std::pair< std::string, size_t > > &colorsIndex, const std::string &toFind) {
133 for (auto &i : colorsIndex) {
134 if (i.first == toFind) {
135 return frame[i.second];
138 throw "WRONG COLOR ATOM NAME TO EVALUATE VECTORS";
141 // функция векторного произведения двух RVec'ов
142 inline void RVecVecMultiply(gmx::RVec &n, const gmx::RVec &a, const gmx::RVec &b) {
143 n[0] = a[1] * b[2] - a[2] * b[1];
144 n[1] = a[2] * b[0] - a[0] * b[2];
145 n[2] = a[0] * b[1] - a[2] * b[0];
148 // поиск угла между двумя RVec'ами
149 inline double RVecAngle(const gmx::RVec &a, const gmx::RVec &b) {
150 return std::acos((a[0] * b[0] + a[1] * b[1] + a[2] * b[2]) / (a.norm() * b.norm()));
153 // вычисление внутренних углов в краске
154 void colorsAnglesEvaluation(const std::vector< gmx::RVec > &frame, const std::vector< std::vector< std::pair< std::string, size_t > > > &colorsIndex,
155 std::vector< colorLocalAngles > &colorStruct) {
156 colorStruct.resize(colorsIndex.size());
157 #pragma omp parallel for ordered schedule(dynamic)
158 for (size_t i = 0; i < colorsIndex.size(); ++i) {
159 colorStruct[i].betaAngles.resize(0);
161 colorStruct[i].a1 = returnRVec(frame, colorsIndex[i], "CAF") - returnRVec(frame, colorsIndex[i], "CAJ") + returnRVec(frame, colorsIndex[i], "CAK") - returnRVec(frame, colorsIndex[i], "CAO");
162 colorStruct[i].a1 /= colorStruct[i].a1.norm();
163 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");
164 colorStruct[i].b1 /= colorStruct[i].b1.norm();
165 RVecVecMultiply(colorStruct[i].n1, colorStruct[i].a1, colorStruct[i].b1);
166 colorStruct[i].n1 /= colorStruct[i].n1.norm();
168 colorStruct[i].a2 = returnRVec(frame, colorsIndex[i], "CAB") - returnRVec(frame, colorsIndex[i], "CBQ") + returnRVec(frame, colorsIndex[i], "CBP") - returnRVec(frame, colorsIndex[i], "CBL");
169 colorStruct[i].a2 /= colorStruct[i].a2.norm();
170 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");
171 colorStruct[i].b2 /= colorStruct[i].b2.norm();
172 RVecVecMultiply(colorStruct[i].n2, colorStruct[i].a2, colorStruct[i].b2);
173 colorStruct[i].n2 *= -1; // для "сонаправленности" векторов нормали
174 colorStruct[i].n2 /= colorStruct[i].n2.norm();
175 colorStruct[i].a12 = RVecAngle(colorStruct[i].a1, colorStruct[i].a2);
176 colorStruct[i].b12 = RVecAngle(colorStruct[i].b1, colorStruct[i].b2);
177 colorStruct[i].n12 = RVecAngle(colorStruct[i].n1, colorStruct[i].n2);
182 // вычисление направляющего вектора в бэта-листе
183 inline void betaListsRVecsEvaluation(const std::vector< gmx::RVec > &frame, const std::vector< std::vector< unsigned int > > &inputBetaLists,
184 std::vector< gmx::RVec > &temp, const std::vector< size_t > &inputCA) {
187 for (const auto &i : inputBetaLists) {
188 tempA = frame[inputCA[i[i.size() - 1]]] + frame[inputCA[i[i.size() - 2]]] - frame[inputCA[i[1]]] - frame[inputCA[i[0]]];
189 tempA /= tempA.norm();
190 temp.push_back(tempA);
194 //// определение близко ли к белку находится краска
195 //bool isNearPeptide(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
196 // /*gmx::AnalysisNeighborhood &nbhood, */const std::vector< size_t > &inputIndex,
197 // const std::vector< std::pair< std::string, size_t > > &inputColor) {
198 // /*gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
199 // gmx::AnalysisNeighborhoodPair pair;*/
201 // for (size_t i = 0; i < inputColor.size(); ++i) {
202 // std::cout << inputColor[i].first << " " << i << " / " << inputColor.size() << std::endl;
203 // gmx::AnalysisNeighborhood nbhood;
204 // nbhood.setCutoff(0.8);
205 // gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
206 // gmx::AnalysisNeighborhoodPair pair;
207 // gmx::AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(inputFrame[inputColor[i].second].as_vec());
209 // while (pairSearch.findNextPair(&pair)) {
210 // std::cout << ++count1 << " ";
211 // for (size_t j = 0; j < inputIndex.size(); ++j) {
212 // if (pair.refIndex() == inputIndex[j]) {
217 // std::cout << inputColor[i].first << " atom done" << std::endl;
222 // определение близко ли к белку находится краска
223 bool isNearPeptide( const std::vector< gmx::RVec > &inputFrame, const std::vector< size_t > &inputIndex,
224 const std::vector< std::pair< std::string, size_t > > &inputColor, const double cutOff) {
225 for (size_t i {0}; i < inputColor.size(); ++i) {
226 for (size_t j {0}; j < inputIndex.size(); ++j) {
227 if ((inputFrame[inputIndex[j]] - inputFrame[inputColor[i].second]).norm() <= cutOff) {
236 // поиск ближайших к краске бэта-листов
237 //inline void searchNearBetaLists(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
238 // gmx::AnalysisNeighborhood &nbhood,
239 // const std::vector< std::vector< unsigned int > > &inputBLists,
240 // const std::vector< std::pair< std::string, size_t > > &inputColor,
241 // std::vector< bool > &outputList, const std::vector< std::vector< size_t > > &inputAminoacids) {
242 // outputList.resize(0);
243 // outputList.resize(inputBLists.size(), false);
244 // gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
245 // gmx::AnalysisNeighborhoodPair pair;
246 // for (const auto &i : inputColor) {
247 // while (nbsearch.startPairSearch(inputFrame[i.second].as_vec()).findNextPair(&pair)) {
248 // for (size_t j = 0; j < inputBLists.size(); ++j) {
249 // for (size_t k = 0; k < inputBLists[j].size(); ++k) {
250 // for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
251 // if (pair.testIndex() == inputAminoacids[inputBLists[j][k]][m]) {
252 // outputList[j] = true;
261 inline void searchNearBetaLists(const std::vector< gmx::RVec > &inputFrame, const std::vector< std::vector< unsigned int > > &inputBLists,
262 const std::vector< std::pair< std::string, size_t > > &inputColor, std::vector< bool > &outputList,
263 const std::vector< std::vector< size_t > > &inputAminoacids, const double cutOff) {
264 outputList.resize(0);
265 outputList.resize(inputBLists.size(), false);
266 for (size_t i {0}; i < inputColor.size(); ++i) {
267 for (size_t j = 0; j < inputBLists.size(); ++j) {
268 for (size_t k = 0; k < inputBLists[j].size(); ++k) {
269 for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
270 if ((inputFrame[inputAminoacids[inputBLists[j][k]][m]] - inputFrame[inputColor[i].second]).norm() <= cutOff) {
271 outputList[j] = true;
272 m = inputAminoacids[inputBLists[j][k]].size() + 1;
273 k = inputBLists[j].size() + 1;
281 // определение углов между краской и направляющим вектором бэта-листа
282 inline void computeAnglesColorsVsBeta(const gmx::RVec &inputBetaRVec, colorLocalAngles &colorFormation) {
283 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a1));
284 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b1));
285 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n1));
286 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a2));
287 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b2));
288 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n2));
291 // функция записи в файл значений углов для кадра
292 void anglesFileDump(const int frameNum, const std::string &output, const std::vector< bool > &toPeptide, const std::vector< colorLocalAngles > &colorFormation) {
293 std::ofstream file(output, std::ofstream::ate);
295 std::vector< double > betaTemp;
297 file << "frame =" << std::setw(8) << frameNum << std::endl;
298 for (size_t i = 0; i < colorFormation.size(); ++i) {
299 file << "color #" << std::setw(3) << i;
301 file << std::setw(4) << "yes";
303 file << std::setw(4) << "no";
305 file << std::setw(7) << std::setprecision(2) << colorFormation[i].a12 << colorFormation[i].b12 << colorFormation[i].n12;
306 temp = colorFormation[i].betaAngles.size() / 6;
308 file << std::setw(4) << 0;
310 betaTemp.resize(6, 0.); // magic number, meh
311 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
312 betaTemp[j % 6] += colorFormation[i].betaAngles[j];
314 for (size_t j = 0; j < betaTemp.size(); ++j) {
317 file << std::setw(4) << temp;
318 for (size_t j = 0; j < betaTemp.size(); ++j) {
319 file << std::setw(7) << std::setprecision(2) << betaTemp[j];
321 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
322 file << std::setw(7) << std::setprecision(2) << colorFormation[i].betaAngles[j];
331 * \ingroup module_trajectoryanalysis
333 class colorVec : public gmx::TrajectoryAnalysisModule
340 //! Set the options and setting
341 virtual void initOptions(gmx::IOptionsContainer *options,
342 gmx::TrajectoryAnalysisSettings *settings);
344 //! First routine called by the analysis framework
345 // virtual void initAnalysis(const t_trxframe &fr, t_pbc *pbc);
346 virtual void initAnalysis(const gmx::TrajectoryAnalysisSettings &settings,
347 const gmx::TopologyInformation &top);
349 //! Call for each frame of the trajectory
350 // virtual void analyzeFrame(const t_trxframe &fr, t_pbc *pbc);
351 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
352 gmx::TrajectoryAnalysisModuleData *pdata);
354 //! Last routine called by the analysis framework
355 // virtual void finishAnalysis(t_pbc *pbc);
356 virtual void finishAnalysis(int nframes);
358 //! Routine to write output, that is additional over the built-in
359 virtual void writeOutput();
363 gmx::SelectionList sel_;
364 std::string fnOut {"name"}; // selectable
365 std::string fnBetaListsDat; // selectable
366 float effRad {0.8}; // selectable
367 std::vector< size_t > index;
368 std::vector< size_t > indexCA;
369 std::vector< std::vector< size_t > > aminoacidsIndex;
370 std::vector< std::vector< std::pair< std::string, size_t > > > colorsNames;
371 std::vector< std::vector< std::vector< unsigned int > > > betaLists;
372 gmx::AnalysisNeighborhood nb_;
374 // Copy and assign disallowed by base.
377 colorVec::colorVec(): TrajectoryAnalysisModule()
381 colorVec::~colorVec()
394 colorVec::initOptions( gmx::IOptionsContainer *options,
395 gmx::TrajectoryAnalysisSettings *settings)
397 static const char *const desc[] = {
398 "[THISMODULE] to be done"
400 // Add the descriptive text (program help text) to the options
401 settings->setHelpText(desc);
402 // Add option for selection list
403 options->addOption(gmx::SelectionOption("sel")
405 .required().dynamicMask().multiValue()
406 .description("select pepride and colors / -sf"));
407 // Add option for input file names
408 options->addOption(gmx::StringOption("dat")
409 .store(&fnBetaListsDat)
410 .description("a file to make dynamic beta lists"));
411 // Add option for output file name
412 options->addOption(gmx::StringOption("out")
414 .description("Index file for the algorithm output."));
415 // Add option for effRad constant
416 options->addOption(gmx::FloatOption("efRad")
418 .description("max distance from colors to peptide in nm to consider to be \"near\""));
419 // Control input settings
420 settings->setFlags(gmx::TrajectoryAnalysisSettings::efNoUserPBC);
421 settings->setFlag(gmx::TrajectoryAnalysisSettings::efUseTopX);
422 //settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
423 settings->setPBC(true);
427 colorVec::initAnalysis( const gmx::TrajectoryAnalysisSettings &settings,
428 const gmx::TopologyInformation &top)
430 // считывание индекса
432 for (gmx::ArrayRef< const int >::iterator ai {sel_.front().atomIndices().begin()}; (ai < sel_.front().atomIndices().end()); ai++) {
433 index.push_back(static_cast< size_t >(*ai));
435 // считывание индекса
437 for (gmx::ArrayRef< const int >::iterator ai {sel_[1].atomIndices().begin()}; (ai < sel_[2].atomIndices().end()); ai++) {
438 index.push_back(static_cast< size_t >(*ai));
441 colorsNames.resize(sel_.size() - 2);
442 for (size_t i = 2; i < sel_.size(); ++i) {
443 for (gmx::ArrayRef< const int >::iterator ai {sel_[i].atomIndices().begin()}; (ai < sel_[i].atomIndices().end()); ai++) {
444 colorsNames[i - 2].push_back(std::make_pair(*(top.atoms()->atomname[*ai]), static_cast< size_t >(*ai)));
447 // разбор dat файла для создания бэта листов
448 betaListDigestion(fnBetaListsDat, betaLists);
449 // разбор топологии для индексации бета листов
450 aminoacidsIndexation(index, top, aminoacidsIndex);
451 // задание радиуса рассматриваемых соседей
452 nb_.setCutoff(effRad);
454 * формально можно сделать:
455 * найти соотношение между именами для углов и индексными номерами
456 * заполнить std::vector< std::vector< size_t > > nameToIndex;
457 * и в последствии считать:
458 * a1 = frame[nameToIndex[0][1] + ... - ... - ...
459 * b1 a2 b2 по аналогии только для [@<-[1, 2, 3]]
465 colorVec::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, gmx::TrajectoryAnalysisModuleData *pdata)
467 std::cout << "\tFrame analisis start ..." << std::endl;
468 std::vector< gmx::RVec > trajectoryFrame;
469 trajectoryFrame.resize(0);
470 // считывания текущего фрейма траектории
471 for (size_t i {0}; i < index.size(); ++i) {
472 trajectoryFrame.push_back(fr.x[index[i]]);
474 // подсчёт углов в красках
475 std::vector< colorLocalAngles > colorFormation;
476 std::cout << "\t\tColors' angles evaluation." << std::endl;
477 colorsAnglesEvaluation(trajectoryFrame, colorsNames, colorFormation);
478 // рассчёт положения относительно белка
480 * формально можно совместить определение близости с белком и определение ближайших бэта-листов
481 * для этого думаю нужно как-то соотнести или сделать соотношение между индексом и бэта-листами (т.е. хранить что бы за О(1) делать)
485 std::vector< bool > colorsToPeptide;
486 colorsToPeptide.resize(0);
487 colorsToPeptide.resize(colorsNames.size(), false);
488 std::cout << "\t\tWhich colors are \"near\" the pepride mass." << std::endl;
489 for (size_t i = 0; i < colorsNames.size(); ++i) {
490 colorsToPeptide[i] = isNearPeptide(trajectoryFrame, index, colorsNames[i], effRad * 20);
492 // расчёт угла и среднего угла с ближайшими бета листами
493 std::vector< std::vector< bool > > colorsToBeta;
494 colorsToBeta.resize(0);
495 colorsToBeta.resize(colorsNames.size());
496 std::vector< std::vector< double > > colorsToBetaAngles;
497 colorsToBetaAngles.resize(0);
498 std::vector< gmx::RVec > betaListsRVecs;
499 std::cout << "\t\tBeta-lists' RVecs search." << std::endl;
500 betaListsRVecsEvaluation(trajectoryFrame, betaLists[frnr], betaListsRVecs, indexCA);
501 std::cout << "\t\tSearching nearby beta-lists." << std::endl;
502 for (size_t i = 0; i < colorsToPeptide.size(); ++i) {
503 if (colorsToPeptide[i]) {
504 searchNearBetaLists(trajectoryFrame, betaLists[frnr], colorsNames[i], colorsToBeta[i], aminoacidsIndex, effRad * 20);
507 std::cout << "\t\tComputing angles colors vs betas." << std::endl;
508 for (size_t i = 0; i < colorsToBeta.size(); ++i) {
509 for (size_t j = 0; j < colorsToBeta[i].size(); ++j) {
510 if (colorsToBeta[i][j]) {
511 computeAnglesColorsVsBeta(betaListsRVecs[j], colorFormation[i]);
515 // вывод в файл(ы) информацию для фрейма
516 std::cout << "\t\tDumping data." << std::endl;
517 anglesFileDump(frnr, fnOut, colorsToPeptide, colorFormation);
518 std::cout << "\tFrame analysed." << std::endl;
522 colorVec::finishAnalysis(int nframes)
528 colorVec::writeOutput()
532 * frame #<current frame number>
533 * 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>]
536 std::cout << "\n\t colorAngles finished successfully" << std::endl;
540 * The main function for the analysis template.
543 main(int argc, char *argv[])
545 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<colorVec>(argc, argv);