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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>
46 #include <gromacs/pbcutil/pbc.h>
57 // структура углов для одной краски
58 struct colorLocalAngles {
59 gmx::RVec a1{0., 0., 0.}, a2{0., 0., 0.};
60 gmx::RVec b1{0., 0., 0.}, b2{0., 0., 0.};
61 gmx::RVec n1{0., 0., 0.}, n2{0., 0., 0.};
62 double a12 {0}, b12 {0}, n12 {0};
63 std::vector< double > betaAngles;
66 // функция парсинга одной строки
67 void parseBetaListDATLine(const std::string ¤tLine, std::vector< std::vector< unsigned int > > &localInputBL) {
68 size_t equalCount = 0;
69 std::vector< unsigned int > a;
71 for (size_t i = 0; i < currentLine.size(); ++i) {
72 if (currentLine[i] == '=') { // подсчитываем число "пустых" символов
76 for (size_t j = i + 1; j < currentLine.size(); ++j) {
77 if (currentLine[j] == 'B' || currentLine[j] == 'E') {
84 localInputBL.push_back(a);
85 for (size_t j = i; j <= temp; ++j) {
86 localInputBL.back().push_back(j - equalCount);
94 // функция нахождения бета-листов в структуре по файлу ДССП
95 void betaListDigestion(const std::string &inputFile, std::vector< std::vector< std::vector< unsigned int > > > &inputBL) {
97 std::ifstream file(inputFile);
99 getline(file, line); // считываем число в первой строке - кол-во осмысленных элементов в строках - нам не нужно
101 if (line.size() > 3) {
103 inputBL.resize(inputBL.size() + 1);
104 parseBetaListDATLine(line, inputBL.back());
107 } while (line.size() > 3);
109 throw "DSSP DAT FILE IS EMPTY";
114 // функция выделения индексов для бэталистов
115 inline void aminoacidsIndexation(const std::vector< size_t > &inputIndex, const gmx::TopologyInformation &top, std::vector< std::vector< size_t > > &aminoacidsIndex) {
116 aminoacidsIndex.resize(0);
117 for (size_t i = 0; i < inputIndex.size(); ++i) {
118 aminoacidsIndex.resize(std::max(aminoacidsIndex.size(), static_cast< size_t >(top.atoms()->atom[inputIndex[i]].resind + 1)));
119 aminoacidsIndex[top.atoms()->atom[inputIndex[i]].resind].push_back(inputIndex[i]);
123 // функция поиска RVec в кадре по имени->индексу
124 gmx::RVec returnRVec(const std::vector< gmx::RVec > &frame, const std::vector< std::pair< std::string, size_t > > &colorsIndex, const std::string &toFind) {
125 for (auto &i : colorsIndex) {
126 if (i.first == toFind) {
127 return frame[i.second];
130 throw "WRONG COLOR ATOM NAME TO EVALUATE VECTORS";
133 // функция векторного произведения двух RVec'ов
134 inline void RVecVecMultiply(gmx::RVec &n, const gmx::RVec &a, const gmx::RVec &b) {
135 n[0] = a[1] * b[2] - a[2] * b[1];
136 n[1] = a[2] * b[0] - a[0] * b[2];
137 n[2] = a[0] * b[1] - a[2] * b[0];
140 // поиск угла между двумя RVec'ами
141 inline double RVecAngle(const gmx::RVec &a, const gmx::RVec &b) {
142 return std::acos((a[0] * b[0] + a[1] * b[1] + a[2] * b[2]) / (a.norm() * b.norm())) * 180.0 / 3.14159265;
145 // вычисление внутренних углов в краске
146 void colorsAnglesEvaluation(const std::vector< gmx::RVec > &frame, const std::vector< std::vector< std::pair< std::string, size_t > > > &colorsIndex,
147 std::vector< colorLocalAngles > &colorStruct) {
148 colorStruct.resize(colorsIndex.size());
149 #pragma omp parallel for ordered schedule(dynamic)
150 for (size_t i = 0; i < colorsIndex.size(); ++i) {
151 colorStruct[i].betaAngles.resize(0);
153 colorStruct[i].a1 = returnRVec(frame, colorsIndex[i], "CAF") - returnRVec(frame, colorsIndex[i], "CAJ") + returnRVec(frame, colorsIndex[i], "CAK") - returnRVec(frame, colorsIndex[i], "CAO");
154 colorStruct[i].a1 /= colorStruct[i].a1.norm();
155 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");
156 colorStruct[i].b1 /= colorStruct[i].b1.norm();
157 RVecVecMultiply(colorStruct[i].n1, colorStruct[i].a1, colorStruct[i].b1);
158 colorStruct[i].n1 /= colorStruct[i].n1.norm();
160 colorStruct[i].a2 = returnRVec(frame, colorsIndex[i], "CAB") - returnRVec(frame, colorsIndex[i], "CBQ") + returnRVec(frame, colorsIndex[i], "CBP") - returnRVec(frame, colorsIndex[i], "CBL");
161 colorStruct[i].a2 /= colorStruct[i].a2.norm();
162 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");
163 colorStruct[i].b2 /= colorStruct[i].b2.norm();
164 RVecVecMultiply(colorStruct[i].n2, colorStruct[i].a2, colorStruct[i].b2);
165 colorStruct[i].n2 *= -1; // для "сонаправленности" векторов нормали
166 colorStruct[i].n2 /= colorStruct[i].n2.norm();
167 colorStruct[i].a12 = RVecAngle(colorStruct[i].a1, colorStruct[i].a2);
168 colorStruct[i].b12 = RVecAngle(colorStruct[i].b1, colorStruct[i].b2);
169 colorStruct[i].n12 = RVecAngle(colorStruct[i].n1, colorStruct[i].n2);
174 // вычисление направляющего вектора в бэта-листе
175 inline void betaListsRVecsEvaluation(const std::vector< gmx::RVec > &frame, const std::vector< std::vector< unsigned int > > &inputBetaLists,
176 std::vector< gmx::RVec > &temp, const std::vector< size_t > &inputCA) {
179 for (const auto &i : inputBetaLists) {
180 tempA = frame[inputCA[i[i.size() - 1]]] + frame[inputCA[i[i.size() - 2]]] - frame[inputCA[i[1]]] - frame[inputCA[i[0]]];
181 tempA /= tempA.norm();
182 temp.push_back(tempA);
186 //// определение близко ли к белку находится краска
187 //bool isNearPeptide(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
188 // /*gmx::AnalysisNeighborhood &nbhood, */const std::vector< size_t > &inputIndex,
189 // const std::vector< std::pair< std::string, size_t > > &inputColor) {
190 // /*gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
191 // gmx::AnalysisNeighborhoodPair pair;*/
193 // for (size_t i = 0; i < inputColor.size(); ++i) {
194 // std::cout << inputColor[i].first << " " << i << " / " << inputColor.size() << std::endl;
195 // gmx::AnalysisNeighborhood nbhood;
196 // nbhood.setCutoff(0.8);
197 // gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
198 // gmx::AnalysisNeighborhoodPair pair;
199 // gmx::AnalysisNeighborhoodPairSearch pairSearch = nbsearch.startPairSearch(inputFrame[inputColor[i].second].as_vec());
201 // while (pairSearch.findNextPair(&pair)) {
202 // std::cout << ++count1 << " ";
203 // for (size_t j = 0; j < inputIndex.size(); ++j) {
204 // if (pair.refIndex() == inputIndex[j]) {
209 // std::cout << inputColor[i].first << " atom done" << std::endl;
214 // определение близко ли к белку находится краска
215 bool isNearPeptide( const t_pbc *inputPBC,
216 const std::vector< gmx::RVec > &inputFrame, const std::vector< size_t > &inputIndex,
217 const std::vector< std::pair< std::string, size_t > > &inputColor, const double cutOff) {
219 for (size_t i {0}; i < inputColor.size(); ++i) {
220 for (size_t j {0}; j < inputIndex.size(); ++j) {
221 pbc_dx(inputPBC, inputFrame[inputIndex[j]], inputFrame[inputColor[i].second], tempRVec);
222 if (tempRVec.norm() <= cutOff) {
230 // поиск ближайших к краске бэта-листов
231 //inline void searchNearBetaLists(const t_trxframe &fr, const t_pbc *pbc, const std::vector< gmx::RVec > &inputFrame,
232 // gmx::AnalysisNeighborhood &nbhood,
233 // const std::vector< std::vector< unsigned int > > &inputBLists,
234 // const std::vector< std::pair< std::string, size_t > > &inputColor,
235 // std::vector< bool > &outputList, const std::vector< std::vector< size_t > > &inputAminoacids) {
236 // outputList.resize(0);
237 // outputList.resize(inputBLists.size(), false);
238 // gmx::AnalysisNeighborhoodSearch nbsearch = nbhood.initSearch(pbc, gmx::AnalysisNeighborhoodPositions(fr.x, fr.natoms));
239 // gmx::AnalysisNeighborhoodPair pair;
240 // for (const auto &i : inputColor) {
241 // while (nbsearch.startPairSearch(inputFrame[i.second].as_vec()).findNextPair(&pair)) {
242 // for (size_t j = 0; j < inputBLists.size(); ++j) {
243 // for (size_t k = 0; k < inputBLists[j].size(); ++k) {
244 // for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
245 // if (pair.testIndex() == inputAminoacids[inputBLists[j][k]][m]) {
246 // outputList[j] = true;
255 inline void searchNearBetaLists(const t_pbc *inputPBC,
256 const std::vector< gmx::RVec > &inputFrame, const std::vector< std::vector< unsigned int > > &inputBLists,
257 const std::vector< std::pair< std::string, size_t > > &inputColor, std::vector< bool > &outputList,
258 const std::vector< std::vector< size_t > > &inputAminoacids, const double cutOff) {
259 outputList.resize(0);
260 outputList.resize(inputBLists.size(), false);
262 for (size_t i {0}; i < inputColor.size(); ++i) {
263 for (size_t j = 0; j < inputBLists.size(); ++j) {
264 for (size_t k = 0; k < inputBLists[j].size(); ++k) {
265 for (size_t m = 0; m < inputAminoacids[inputBLists[j][k]].size(); ++m) {
266 pbc_dx(inputPBC, inputFrame[inputAminoacids[inputBLists[j][k]][m]], inputFrame[inputColor[i].second], tempRVec);
267 if (tempRVec.norm() <= cutOff) {
268 outputList[j] = true;
277 // определение углов между краской и направляющим вектором бэта-листа
278 inline void computeAnglesColorsVsBeta(const gmx::RVec &inputBetaRVec, colorLocalAngles &colorFormation) {
279 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a1));
280 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b1));
281 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n1));
282 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.a2));
283 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.b2));
284 colorFormation.betaAngles.push_back(RVecAngle(inputBetaRVec, colorFormation.n2));
287 // функция записи в файл значений углов для кадра
288 void anglesFileDump(const int frameNum, const std::string &output, const std::vector< bool > &toPeptide, const std::vector< colorLocalAngles > &colorFormation) {
289 std::ofstream file(output, std::ofstream::app);
290 file << "frame =" << std::setw(8) << frameNum << std::endl;
291 for (size_t i = 0; i < colorFormation.size(); ++i) {
292 file << "color #" << std::setw(3) << i;
294 file << std::setw(4) << "yes";
296 file << std::setw(4) << "no";
299 file << std::setw(8) << std::setprecision(5) << colorFormation[i].a12;
300 file << std::setw(8) << std::setprecision(5) << colorFormation[i].b12;
301 file << std::setw(8) << std::setprecision(5) << colorFormation[i].n12;
302 if (colorFormation[i].betaAngles.size() == 0) {
303 file << std::setw(4) << 0;
305 int temp = colorFormation[i].betaAngles.size() / 6;
306 std::vector< double > betaTemp;
308 betaTemp.resize(6, 0.); // magic number, meh
309 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
310 betaTemp[j % 6] += colorFormation[i].betaAngles[j];
312 for (size_t j = 0; j < betaTemp.size(); ++j) {
313 betaTemp[j] /= static_cast< double >(temp);
315 file << std::setw(4) << temp;
316 for (size_t j = 0; j < betaTemp.size(); ++j) {
317 file << std::setw(8) << std::setprecision(5) << betaTemp[j];
319 for (size_t j = 0; j < colorFormation[i].betaAngles.size(); ++j) {
320 file << std::setw(8) << std::setprecision(5) << colorFormation[i].betaAngles[j];
329 * \ingroup module_trajectoryanalysis
331 class colorVec : public gmx::TrajectoryAnalysisModule
338 //! Set the options and setting
339 virtual void initOptions(gmx::IOptionsContainer *options,
340 gmx::TrajectoryAnalysisSettings *settings);
342 //! First routine called by the analysis framework
343 // virtual void initAnalysis(const t_trxframe &fr, t_pbc *pbc);
344 virtual void initAnalysis(const gmx::TrajectoryAnalysisSettings &settings,
345 const gmx::TopologyInformation &top);
347 //! Call for each frame of the trajectory
348 // virtual void analyzeFrame(const t_trxframe &fr, t_pbc *pbc);
349 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
350 gmx::TrajectoryAnalysisModuleData *pdata);
352 //! Last routine called by the analysis framework
353 // virtual void finishAnalysis(t_pbc *pbc);
354 virtual void finishAnalysis(int nframes);
356 //! Routine to write output, that is additional over the built-in
357 virtual void writeOutput();
361 gmx::SelectionList sel_;
362 std::string fnOut {"name"}; // selectable
363 std::string fnBetaListsDat; // selectable
364 float effRad {0.8}; // selectable
365 std::vector< size_t > index;
366 std::vector< size_t > indexCA;
367 std::vector< std::vector< size_t > > aminoacidsIndex;
368 std::vector< std::vector< std::pair< std::string, size_t > > > colorsNames;
369 std::vector< std::vector< std::vector< unsigned int > > > betaLists;
370 gmx::AnalysisNeighborhood nb_;
372 // Copy and assign disallowed by base.
375 colorVec::colorVec(): TrajectoryAnalysisModule()
379 colorVec::~colorVec()
392 colorVec::initOptions( gmx::IOptionsContainer *options,
393 gmx::TrajectoryAnalysisSettings *settings)
395 static const char *const desc[] = {
396 "[THISMODULE] to be done"
398 // Add the descriptive text (program help text) to the options
399 settings->setHelpText(desc);
400 // Add option for selection list
401 options->addOption(gmx::SelectionOption("sel")
403 .required().dynamicMask().multiValue()
404 .description("select pepride and colors / -sf"));
405 // Add option for input file names
406 options->addOption(gmx::StringOption("dat")
407 .store(&fnBetaListsDat)
408 .description("a file to make dynamic beta lists"));
409 // Add option for output file name
410 options->addOption(gmx::StringOption("out")
412 .description("Index file for the algorithm output."));
413 // Add option for effRad constant
414 options->addOption(gmx::FloatOption("efRad")
416 .description("max distance from colors to peptide in nm to consider to be \"near\""));
417 // Control input settings
418 settings->setFlags(gmx::TrajectoryAnalysisSettings::efNoUserPBC);
419 settings->setFlag(gmx::TrajectoryAnalysisSettings::efUseTopX);
420 //settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
421 settings->setPBC(true);
425 colorVec::initAnalysis( const gmx::TrajectoryAnalysisSettings &settings,
426 const gmx::TopologyInformation &top)
428 // считывание индекса
430 for (gmx::ArrayRef< const int >::iterator ai {sel_.front().atomIndices().begin()}; (ai < sel_.front().atomIndices().end()); ai++) {
431 index.push_back(static_cast< size_t >(*ai));
433 // считывание индекса
435 for (gmx::ArrayRef< const int >::iterator ai {sel_[1].atomIndices().begin()}; (ai < sel_[1].atomIndices().end()); ai++) {
436 indexCA.push_back(static_cast< size_t >(*ai));
439 colorsNames.resize(sel_.size() - 2);
440 for (size_t i = 2; i < sel_.size(); ++i) {
441 for (gmx::ArrayRef< const int >::iterator ai {sel_[i].atomIndices().begin()}; (ai < sel_[i].atomIndices().end()); ai++) {
442 colorsNames[i - 2].push_back(std::make_pair(*(top.atoms()->atomname[*ai]), static_cast< size_t >(*ai)));
445 // разбор dat файла для создания бэта листов
446 betaListDigestion(fnBetaListsDat, betaLists);
447 // разбор топологии для индексации бета листов
448 aminoacidsIndexation(index, top, aminoacidsIndex);
449 // задание радиуса рассматриваемых соседей
450 nb_.setCutoff(effRad);
451 // вывод базовых значений
452 std::cout << std::endl;
453 std::cout << "effective radius = " << std::setw(20) << effRad << std::endl;
454 std::cout << "DAT file = " << std::setw(20) << fnBetaListsDat << std::endl;
455 std::cout << "output file = " << std::setw(20) << fnOut << std::endl;
456 std::cout << "peptide atoms # = " << std::setw(20) << index.size() << std::endl;
457 std::cout << "CA-atmos # = " << std::setw(10) << indexCA.size() << std::endl;
458 std::cout << "Beta frames = " << std::setw(10) << betaLists.size() << std::endl;
459 std::cout << "residue # = " << std::setw(10) << aminoacidsIndex.size() << std::endl;
460 std::cout << "colors # = " << std::setw(10) << colorsNames.size() << std::endl;
463 * формально можно сделать:
464 * найти соотношение между именами для углов и индексными номерами
465 * заполнить std::vector< std::vector< size_t > > nameToIndex;
466 * и в последствии считать:
467 * a1 = frame[nameToIndex[0][1] + ... - ... - ...
468 * b1 a2 b2 по аналогии только для [@<-[1, 2, 3]]
474 colorVec::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc, gmx::TrajectoryAnalysisModuleData *pdata)
476 std::vector< gmx::RVec > trajectoryFrame;
477 trajectoryFrame.resize(0);
478 // считывания текущего фрейма траектории
479 for (size_t i {0}; i < fr.natoms; ++i) {
480 trajectoryFrame.push_back(fr.x[i]);
482 // подсчёт углов в красках
483 std::vector< colorLocalAngles > colorFormation;
484 colorsAnglesEvaluation(trajectoryFrame, colorsNames, colorFormation);
485 // рассчёт положения относительно белка
487 * формально можно совместить определение близости с белком и определение ближайших бэта-листов
488 * для этого думаю нужно как-то соотнести или сделать соотношение между индексом и бэта-листами (т.е. хранить что бы за О(1) делать)
494 std::vector< bool > colorsToPeptide;
495 colorsToPeptide.resize(0);
496 colorsToPeptide.resize(colorsNames.size(), false);
497 for (size_t i = 0; i < colorsNames.size(); ++i) {
498 colorsToPeptide[i] = isNearPeptide(pbc, trajectoryFrame, index, colorsNames[i], effRad);
500 // расчёт угла и среднего угла с ближайшими бета листами
501 std::vector< std::vector< bool > > colorsToBeta;
502 colorsToBeta.resize(0);
503 colorsToBeta.resize(colorsNames.size());
504 std::vector< std::vector< double > > colorsToBetaAngles;
505 colorsToBetaAngles.resize(0);
506 std::vector< gmx::RVec > betaListsRVecs;
507 betaListsRVecsEvaluation(trajectoryFrame, betaLists[frnr], betaListsRVecs, indexCA);
508 for (size_t i = 0; i < colorsToPeptide.size(); ++i) {
509 if (colorsToPeptide[i]) {
510 searchNearBetaLists(pbc, trajectoryFrame, betaLists[frnr], colorsNames[i], colorsToBeta[i], aminoacidsIndex, effRad);
513 for (size_t i = 0; i < colorsToBeta.size(); ++i) {
514 for (size_t j = 0; j < colorsToBeta[i].size(); ++j) {
515 if (colorsToBeta[i][j]) {
516 computeAnglesColorsVsBeta(betaListsRVecs[j], colorFormation[i]);
520 // вывод в файл(ы) информацию для фрейма
521 anglesFileDump(frnr, fnOut, colorsToPeptide, colorFormation);
522 std::cout << std::endl << "frame number " << frnr;
526 colorVec::finishAnalysis(int nframes)
532 colorVec::writeOutput()
536 * frame #<current frame number>
537 * 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>]
543 * The main function for the analysis template.
546 main(int argc, char *argv[])
548 return gmx::TrajectoryAnalysisCommandLineRunner::runAsMain<colorVec>(argc, argv);