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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 for (const auto &i : inputColor) {
199 gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
200 gmx::AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(inputFrame[i.second].as_vec());
201 gmx::AnalysisNeighborhoodPair pair;
202 std::cout << std::endl << i.first << std::endl;
204 while (pairSearch.findNextPair(&pair)) {
205 std::cout << " " << ++count1;
206 for (const auto &j : inputIndex) {
207 if (pair.refIndex() == j) {
216 // поиск ближайших к краске бэта-листов
217 inline void searchNearBetaLists(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
218 gmx::AnalysisNeighborhood &nbhood,
219 const std::vector< std::vector< unsigned int > > &inputBLists,
220 const std::vector< std::pair< std::string, size_t > > &inputColor,
221 std::vector< bool > &outputList, const std::vector< std::vector< size_t > > &inputAminoacids) {
222 outputList.resize(0);
223 outputList.resize(inputBLists.size(), false);
224 gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
225 gmx::AnalysisNeighborhoodPair pair;
226 for (const auto &i : inputColor) {
227 while (nbsearch.startPairSearch(inputFrame[i.second].as_vec()).findNextPair(&pair)) {
228 for (size_t j = 0; j < inputBLists.size(); ++j) {
229 for (size_t k = 0; k < inputBLists[j].size(); ++k) {
230 for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
231 if (pair.testIndex() == inputAminoacids[inputBLists[j][k]][m]) {
232 outputList[j] = true;
242 // определение углов между краской и направляющим вектором бэта-листа
243 inline void computeAnglesColorsVsBeta(const gmx::RVec &inputBetaRVec, colorLocalAngles &colorFormation) {
244 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a1));
245 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b1));
246 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n1));
247 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a2));
248 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b2));
249 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n2));
252 // функция записи в файл значений углов для кадра
253 void anglesFileDump(const int frameNum, const std::string &output, const std::vector< bool > &toPeptide, const std::vector< colorLocalAngles > &colorFormation) {
254 std::ofstream file(output);
256 std::vector< double > betaTemp;
258 file << "frame =" << std::setw(8) << frameNum << std::endl;
259 for (size_t i = 0; i < colorFormation.size(); ++i) {
260 file << "color #" << std::setw(3) << i;
262 file << std::setw(4) << "yes";
264 file << std::setw(4) << "no";
266 file << std::setw(7) << std::setprecision(2) << colorFormation[i].a12 << colorFormation[i].b12 << colorFormation[i].n12;
267 temp = colorFormation[i].betaAngles.size() / 6;
269 file << std::setw(4) << 0;
271 betaTemp.resize(6, 0.); // magic number, meh
272 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
273 betaTemp[j % 6] += colorFormation[i].betaAngles[j];
275 for (size_t j = 0; j < betaTemp.size(); ++j) {
278 file << std::setw(4) << temp;
279 for (size_t j = 0; j < betaTemp.size(); ++j) {
280 file << std::setw(7) << std::setprecision(2) << betaTemp[j];
282 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
283 file << std::setw(7) << std::setprecision(2) << colorFormation[i].betaAngles[j];
291 * \ingroup module_trajectoryanalysis
293 class colorVec : public gmx::TrajectoryAnalysisModule
300 //! Set the options and setting
301 virtual void initOptions(gmx::IOptionsContainer *options,
302 gmx::TrajectoryAnalysisSettings *settings);
304 //! First routine called by the analysis framework
305 // virtual void initAnalysis(const t_trxframe &fr, t_pbc *pbc);
306 virtual void initAnalysis(const gmx::TrajectoryAnalysisSettings &settings,
307 const gmx::TopologyInformation &top);
309 //! Call for each frame of the trajectory
310 // virtual void analyzeFrame(const t_trxframe &fr, t_pbc *pbc);
311 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
312 gmx::TrajectoryAnalysisModuleData *pdata);
314 //! Last routine called by the analysis framework
315 // virtual void finishAnalysis(t_pbc *pbc);
316 virtual void finishAnalysis(int nframes);
318 //! Routine to write output, that is additional over the built-in
319 virtual void writeOutput();
323 gmx::SelectionList sel_;
324 std::string fnOut {"name"}; // selectable
325 std::string fnBetaListsDat; // selectable
326 float effRad {0.8}; // selectable
327 std::vector< size_t > index;
328 std::vector< size_t > indexCA;
329 std::vector< std::vector< size_t > > aminoacidsIndex;
330 std::vector< std::vector< std::pair< std::string, size_t > > > colorsNames;
331 std::vector< std::vector< std::vector< unsigned int > > > betaLists;
332 gmx::AnalysisNeighborhood nb_;
334 // Copy and assign disallowed by base.
337 colorVec::colorVec(): TrajectoryAnalysisModule()
341 colorVec::~colorVec()
354 colorVec::initOptions( gmx::IOptionsContainer *options,
355 gmx::TrajectoryAnalysisSettings *settings)
357 static const char *const desc[] = {
358 "[THISMODULE] to be done"
360 // Add the descriptive text (program help text) to the options
361 settings->setHelpText(desc);
362 // Add option for selection list
363 options->addOption(gmx::SelectionOption("sel")
365 .required().dynamicMask().multiValue()
366 .description("select pepride and colors / -sf"));
367 // Add option for input file names
368 options->addOption(gmx::StringOption("dat")
369 .store(&fnBetaListsDat)
370 .description("a file to make dynamic beta lists"));
371 // Add option for output file name
372 options->addOption(gmx::StringOption("out")
374 .description("Index file for the algorithm output."));
375 // Add option for effRad constant
376 options->addOption(gmx::FloatOption("efRad")
378 .description("max distance from colors to peptide in nm to consider to be \"near\""));
379 // Control input settings
380 settings->setFlags(gmx::TrajectoryAnalysisSettings::efNoUserPBC);
381 settings->setFlag(gmx::TrajectoryAnalysisSettings::efUseTopX);
382 //settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
383 settings->setPBC(true);
387 colorVec::initAnalysis( const gmx::TrajectoryAnalysisSettings &settings,
388 const gmx::TopologyInformation &top)
390 // считывание индекса
392 for (gmx::ArrayRef< const int >::iterator ai {sel_.front().atomIndices().begin()}; (ai < sel_.front().atomIndices().end()); ai++) {
393 index.push_back(static_cast< size_t >(*ai));
395 // считывание индекса
397 for (gmx::ArrayRef< const int >::iterator ai {sel_[1].atomIndices().begin()}; (ai < sel_[2].atomIndices().end()); ai++) {
398 index.push_back(static_cast< size_t >(*ai));
401 colorsNames.resize(sel_.size() - 2);
402 for (size_t i = 2; i < sel_.size(); ++i) {
403 for (gmx::ArrayRef< const int >::iterator ai {sel_[i].atomIndices().begin()}; (ai < sel_[i].atomIndices().end()); ai++) {
404 colorsNames[i - 2].push_back(std::make_pair(*(top.atoms()->atomname[*ai]), static_cast< size_t >(*ai)));
407 // разбор dat файла для создания бэта листов
408 betaListDigestion(fnBetaListsDat, betaLists);
409 // разбор топологии для индексации бета листов
410 aminoacidsIndexation(index, top, aminoacidsIndex);
411 // задание радиуса рассматриваемых соседей
412 nb_.setCutoff(effRad);
414 * формально можно сделать:
415 * найти соотношение между именами для углов и индексными номерами
416 * заполнить std::vector< std::vector< size_t > > nameToIndex;
417 * и в последствии считать:
418 * a1 = frame[nameToIndex[0][1] + ... - ... - ...
419 * b1 a2 b2 по аналогии только для [@<-[1, 2, 3]]
425 colorVec::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, gmx::TrajectoryAnalysisModuleData *pdata)
427 std::cout << "\tFrame analisis start ..." << std::endl;
428 std::vector< gmx::RVec > trajectoryFrame;
429 trajectoryFrame.resize(0);
430 // считывания текущего фрейма траектории
431 for (size_t i {0}; i < index.size(); ++i) {
432 trajectoryFrame.push_back(fr.x[index[i]]);
434 // подсчёт углов в красках
435 std::vector< colorLocalAngles > colorFormation;
436 std::cout << "\t\tColors' angles evaluation." << std::endl;
437 colorsAnglesEvaluation(trajectoryFrame, colorsNames, colorFormation);
438 // рассчёт положения относительно белка
440 * формально можно совместить определение близости с белком и определение ближайших бэта-листов
441 * для этого думаю нужно как-то соотнести или сделать соотношение между индексом и бэта-листами (т.е. хранить что бы за О(1) делать)
445 std::vector< bool > colorsToPeptide;
446 colorsToPeptide.resize(0);
447 colorsToPeptide.resize(colorsNames.size(), false);
448 std::cout << "\t\tWhich colors are \"near\" the pepride mass." << std::endl;
449 for (size_t i = 0; i < colorsNames.size(); ++i) {
450 colorsToPeptide[i] = isNearPeptide(fr, pbc, trajectoryFrame, nb_, index, colorsNames[i]);
452 // расчёт угла и среднего угла с ближайшими бета листами
453 std::vector< std::vector< bool > > colorsToBeta;
454 colorsToBeta.resize(0);
455 colorsToBeta.resize(colorsNames.size());
456 std::vector< std::vector< double > > colorsToBetaAngles;
457 colorsToBetaAngles.resize(0);
458 std::vector< gmx::RVec > betaListsRVecs;
459 std::cout << "\t\tBeta-lists' RVecs search." << std::endl;
460 betaListsRVecsEvaluation(trajectoryFrame, betaLists[frnr], betaListsRVecs, indexCA);
461 std::cout << "\t\tSearching nearby beta-lists." << std::endl;
462 for (size_t i = 0; i < colorsToPeptide.size(); ++i) {
463 if (colorsToPeptide[i]) {
464 searchNearBetaLists(fr, pbc, trajectoryFrame, nb_, betaLists[frnr], colorsNames[i], colorsToBeta[i], aminoacidsIndex);
467 std::cout << "\t\tComputing angles colors vs betas." << std::endl;
468 for (size_t i = 0; i < colorsToBeta.size(); ++i) {
469 for (size_t j = 0; j < colorsToBeta[i].size(); ++j) {
470 if (colorsToBeta[i][j]) {
471 computeAnglesColorsVsBeta(betaListsRVecs[j], colorFormation[i]);
475 // вывод в файл(ы) информацию для фрейма
476 std::cout << "\t\tDumping data." << std::endl;
477 anglesFileDump(frnr, fnOut, colorsToPeptide, colorFormation);
478 std::cout << "\tFrame analysed." << std::endl;
482 colorVec::finishAnalysis(int nframes)
488 colorVec::writeOutput()
492 * frame #<current frame number>
493 * 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>]
496 std::cout << "\n\t colorAngles finished successfully" << std::endl;
500 * The main function for the analysis template.
503 main(int argc, char *argv[])
505 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<colorVec>(argc, argv);