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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 There's something wrong with energy calculations of redidues with E ≈ -0
50 #include "dssptools.h"
53 #include "gromacs/math/units.h"
55 #include "gromacs/pbcutil/pbc.h"
56 #include <gromacs/trajectoryanalysis.h>
57 #include "gromacs/trajectoryanalysis/topologyinformation.h"
66 namespace analysismodules
69 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
71 // _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
74 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
76 // return _ResInfo[static_cast<std::size_t>(atomTypeName)];
79 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
80 return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
83 secondaryStructures::secondaryStructures(){
85 void secondaryStructures::initiateSearch(const std::vector<ResInfo> &ResInfoMatrix, const bool PiHelicesPreferencez){
86 SecondaryStructuresStatusMap.resize(0);
87 SecondaryStructuresStringLine.resize(0);
88 std::vector<std::size_t> temp; temp.resize(0),
89 PiHelixPreference = PiHelicesPreferencez;
90 ResInfoMap = &ResInfoMatrix;
91 SecondaryStructuresStatusMap.resize(ResInfoMatrix.size());
92 SecondaryStructuresStringLine.resize(ResInfoMatrix.size(), '~');
95 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName){
96 SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = true;
99 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
100 TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
103 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
104 return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
107 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
108 return breakPartners[0] == partner || breakPartners[1] == partner;
111 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
112 return TurnsStatusArray[static_cast<std::size_t>(turn)];
115 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
116 if (breakPartners[0] == nullptr){
117 breakPartners[0] = breakPartner;
120 breakPartners[1] = breakPartner;
122 setStatus(secondaryStructureTypes::Break);
125 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
126 if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
127 (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
128 (*ResInfoMap)[Acceptor].info == nullptr ){
129 std::cout << "Bad hbond check. Reason(s): " ;
130 if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
131 std::cout << "Donor has no acceptor[0]; ";
133 if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
134 std::cout << "Donor has no acceptor[1]; ";
136 if ( (*ResInfoMap)[Acceptor].info == nullptr ){
137 std::cout << "No info about acceptor; ";
139 std::cout << std::endl;
142 // else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
143 // (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
144 // (*ResInfoMap)[Donor].info == nullptr )) {
145 // std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
146 // std::cout << "Donor's acceptors' nr are = " << (*ResInfoMap)[Donor].acceptor[0]->nr << " (chain " << (*ResInfoMap)[Donor].acceptor[0]->chainid << ") , " << (*ResInfoMap)[Donor].acceptor[1]->nr << " (chain " << (*ResInfoMap)[Donor].acceptor[1]->chainid << ")" << std::endl;
147 // std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
148 // std::cout << "Acceptors's donors' nr are = " << (*ResInfoMap)[Acceptor].donor[0]->nr << " (chain " << (*ResInfoMap)[Acceptor].donor[0]->chainid << ") , " << (*ResInfoMap)[Acceptor].donor[1]->nr << " (chain " << (*ResInfoMap)[Acceptor].donor[1]->chainid << ")" << std::endl;
149 // std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
150 // if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
151 // ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
152 // std::cout << "HBond Exist" << std::endl;
156 // std::cout << "Bad hbond check. Reason(s): " ;
157 // if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
158 // std::cout << "Acceptor has no donor[0]; ";
160 // if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
161 // std::cout << "Acceptor has no donor[1]; ";
163 // if ( (*ResInfoMap)[Donor].info == nullptr ){
164 // std::cout << "No info about donor; ";
166 // std::cout << std::endl;
169 return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
170 ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
175 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
176 std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
182 if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
183 std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
190 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
191 if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
192 return bridgeTypes::None;
194 if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
195 if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
196 return bridgeTypes::ParallelBridge;
198 else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
199 return bridgeTypes::AntiParallelBridge;
202 return bridgeTypes::None;
205 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
206 for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
207 for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
208 bridgeTypes type {calculateBridge(i, j)};
209 if (type == bridgeTypes::None){
227 // for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
228 // for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
229 // if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
230 // if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1]) ||
231 // (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
232 // Bridge[i].push_back(j);
234 // if ((HBondsMap[i][j] && HBondsMap[j][i]) ||
235 // (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
236 // AntiBridge[i].push_back(j);
241 // for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
242 // if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
243 // setStatus(i, secondaryStructureTypes::Bulge);
246 // for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
247 // for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
252 // for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
253 // if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
254 // for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
255 // for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
256 // if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
257 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
258 // && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
259 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
262 // for (std::size_t k{ 0 }; k <= i - j; ++k){
263 // setStatus(i + k, secondaryStructureTypes::Ladder);
267 // for (std::size_t k{ 0 }; k <= j - i; ++k){
268 // setStatus(i + k, secondaryStructureTypes::Ladder);
281 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
282 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
283 std::size_t stride {static_cast<std::size_t>(i) + 3};
284 std::cout << "Testing Helix_" << stride << std::endl;
285 for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
286 std::cout << "Testing " << j << " and " << j + stride << std::endl;
287 if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
288 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
289 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
291 for (std::size_t k {1}; k < stride; ++k){
292 if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
293 SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
294 // SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
299 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
300 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
303 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
309 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
310 std::size_t stride {static_cast<std::size_t>(i) + 3};
311 for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
312 if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
313 (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
315 secondaryStructureTypes Helix;
317 case turnsTypes::Turn_3:
318 for (std::size_t k {0}; empty && k < stride; ++k){
319 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
321 Helix = secondaryStructureTypes::Helix_3;
323 case turnsTypes::Turn_5:
324 for (std::size_t k {0}; empty && k < stride; ++k){
325 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
327 Helix = secondaryStructureTypes::Helix_5;
330 Helix = secondaryStructureTypes::Helix_4;
333 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
334 for(std::size_t k {0}; k < stride; ++k ){
335 SecondaryStructuresStatusMap[j + k].setStatus(Helix);
342 for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
343 if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
345 for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
346 std::size_t stride {static_cast<std::size_t>(i) + 3};
347 for(std::size_t k {1}; k < stride; ++k){
348 isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
353 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
360 void secondaryStructures::analyzePPHelicesPatterns(){}
362 std::string secondaryStructures::patternSearch(){
365 // analyzeBridgesAndLaddersPatterns();
366 analyzeTurnsAndHelicesPatterns();
367 // analyzePPHelicesPatterns();
369 // for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
370 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
373 // std::cout.precision(5);
374 // for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
375 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
376 // if ( (*ResInfoMap)[i].donor[0] != nullptr ){
377 // std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
380 // std::cout << " has no donor[0] and" ;
382 // if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
383 // std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
386 // std::cout << " has no acceptor[0]" ;
388 // std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
389 // if ( (*ResInfoMap)[i].donor[1] != nullptr ){
390 // std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
393 // std::cout << " has no donor[1] and" ;
395 // if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
396 // std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
399 // std::cout << " has no acceptor[1]" ;
405 for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
406 for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
407 if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
408 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
415 if(SecondaryStructuresStatusMap.size() > 1){
416 for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
417 if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
418 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
419 SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
425 return SecondaryStructuresStringLine;
428 secondaryStructures::~secondaryStructures(){
429 SecondaryStructuresStatusMap.resize(0);
430 SecondaryStructuresStringLine.resize(0);
433 DsspTool::DsspStorage::DsspStorage(){
434 storaged_data.resize(0);
437 void DsspTool::DsspStorage::clearAll(){
438 storaged_data.resize(0);
441 std::mutex DsspTool::DsspStorage::mx;
443 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
444 std::lock_guard<std::mutex> guardian(mx);
445 std::pair<int, std::string> datapair(frnr, data);
446 storaged_data.push_back(datapair);
449 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
450 std::sort(storaged_data.begin(), storaged_data.end());
451 return storaged_data;
454 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
455 cutoff = cutoff_init;
458 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
459 while (coordinate < 0) {
460 coordinate += vector_length;
462 while (coordinate >= vector_length) {
463 coordinate -= vector_length;
467 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
476 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
477 rvec coordinates, box_vector_length;
478 num_of_miniboxes.resize(0);
479 num_of_miniboxes.resize(3);
480 for (std::size_t i{XX}; i <= ZZ; ++i) {
481 box_vector_length[i] = std::sqrt(
482 std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
483 num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
485 MiniBoxesMap.resize(0);
486 MiniBoxesReverseMap.resize(0);
487 MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
488 num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
489 num_of_miniboxes[ZZ], std::vector<std::size_t>(
491 MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
492 for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
493 for (std::size_t j{XX}; j <= ZZ; ++j) {
494 coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
495 FixAtomCoordinates(coordinates[j], box_vector_length[j]);
497 MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
498 coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
499 for (std::size_t j{XX}; j <= ZZ; ++j){
500 MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
505 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
506 GetMiniBoxesMap(fr, IndexMap);
507 MiniBoxSize[XX] = MiniBoxesMap.size();
508 MiniBoxSize[YY] = MiniBoxesMap.front().size();
509 MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
511 PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
512 ResiI = PairMap.begin();
513 ResiJ = ResiI->begin();
515 for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
516 for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
517 for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
518 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
519 for (std::size_t k{XX}; k <= ZZ; ++k) {
520 fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
521 ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
523 for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
524 if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
525 PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
526 PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
535 bool alternateNeighborhoodSearch::findNextPair(){
541 for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
542 for(; ResiJ != ResiI->end(); ++ResiJ){
544 resiIpos = ResiI - PairMap.begin();
545 resiJpos = ResiJ - ResiI->begin();
546 if ( ResiJ != ResiI->end() ){
549 else if (ResiI != PairMap.end()) {
551 ResiJ = ResiI->begin();
564 std::size_t alternateNeighborhoodSearch::getResiI() const {
568 std::size_t alternateNeighborhoodSearch::getResiJ() const {
573 DsspTool::DsspStorage DsspTool::Storage;
575 DsspTool::DsspTool(){
578 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
580 const float benddegree{ 70.0 }, maxdist{ 2.5 };
581 float degree{ 0 }, vdist{ 0 }, vprod{ 0 };
582 gmx::RVec a{ 0, 0, 0 }, b{ 0, 0, 0 };
583 for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
585 if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
586 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
591 PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
592 PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
594 // std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
597 for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
599 if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
600 PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
601 PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
602 PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
607 for (int j{ 0 }; j < 3; ++j)
609 a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
610 - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
611 b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
612 - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
614 vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
615 vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
616 IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
619 * gmx::c_angstrom / gmx::c_nano
620 * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
621 IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
624 * gmx::c_angstrom / gmx::c_nano;
625 degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
626 if (degree > benddegree)
628 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
633 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
635 const t_trxframe& fr,
639 * DSSP uses eq from dssp 2.x
640 * kCouplingConstant = 27.888, // = 332 * 0.42 * 0.2
641 * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
645 * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
649 if (CalculateAtomicDistances(
650 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
651 >= minimalCAdistance)
656 const float kCouplingConstant = 27.888;
657 const float minimalAtomDistance{ 0.5 },
659 float HbondEnergy{ 0 };
660 float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
662 // std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
664 if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
665 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
666 distanceNO = CalculateAtomicDistances(
667 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
668 distanceNC = CalculateAtomicDistances(
669 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
670 if (initParams.addHydrogens){
671 if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
673 float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
674 for (int i{XX}; i <= ZZ; ++i){
675 float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
676 atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
677 atomH[i] += prevCO / prevCODist;
679 distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
680 distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
683 distanceHO = distanceNO;
684 distanceHC = distanceNC;
688 distanceHO = CalculateAtomicDistances(
689 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
690 distanceHC = CalculateAtomicDistances(
691 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
693 if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
694 || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
696 HbondEnergy = minEnergy;
701 * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
704 // std::cout << "CA-CA distance: " << CalculateAtomicDistances(
705 // Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
706 // std::cout << "N-O distance: " << distanceNO << std::endl;
707 // std::cout << "N-C distance: " << distanceNC << std::endl;
708 // std::cout << "H-O distance: " << distanceHO << std::endl;
709 // std::cout << "H-C distance: " << distanceHC << std::endl;
711 HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
713 // if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
714 // HbondEnergy = minEnergy;
717 // std::cout << "Calculated energy = " << HbondEnergy << std::endl;
720 // std::cout << "Donor Is Proline" << std::endl;
723 if (HbondEnergy < Donor.acceptorEnergy[0]){
724 Donor.acceptor[1] = Donor.acceptor[0];
725 Donor.acceptor[0] = Acceptor.info;
726 Donor.acceptorEnergy[0] = HbondEnergy;
728 else if (HbondEnergy < Donor.acceptorEnergy[1]){
729 Donor.acceptor[1] = Acceptor.info;
730 Donor.acceptorEnergy[1] = HbondEnergy;
733 if (HbondEnergy < Acceptor.donorEnergy[0]){
734 Acceptor.donor[1] = Acceptor.donor[0];
735 Acceptor.donor[0] = Donor.info;
736 Acceptor.donorEnergy[0] = HbondEnergy;
738 else if (HbondEnergy < Acceptor.donorEnergy[1]){
739 Acceptor.donor[1] = Donor.info;
740 Acceptor.donorEnergy[1] = HbondEnergy;
745 /* Calculate Distance From B to A */
746 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
748 gmx::RVec r{ 0, 0, 0 };
749 pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
750 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
753 /* Calculate Distance From B to A, where A is only fake coordinates */
754 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
756 gmx::RVec r{ 0, 0, 0 };
757 pbc_dx(pbc, A, fr.x[B], r.as_vec());
758 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
761 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
763 initParams = initParamz;
764 ResInfo _backboneAtoms;
767 int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
769 IndexMap.push_back(_backboneAtoms);
770 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
771 proLINE = *(IndexMap[i].info->name);
772 if( proLINE.compare("PRO") == 0 ){
773 IndexMap[i].is_proline = true;
776 for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
777 if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
780 resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
781 IndexMap.emplace_back(_backboneAtoms);
782 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
783 proLINE = *(IndexMap[i].info->name);
784 if( proLINE.compare("PRO") == 0 ){
785 IndexMap[i].is_proline = true;
789 std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
790 if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
792 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
794 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
796 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
798 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
800 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
802 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
804 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
805 if (initParamz.addHydrogens == true){
806 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
809 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
811 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
816 // if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
817 // || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
818 // std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
822 for (std::size_t j {1}; j < IndexMap.size(); ++j){
823 IndexMap[j].prevResi = &(IndexMap[j - 1]);
825 IndexMap[j - 1].nextResi = &(IndexMap[j]);
827 // std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
828 // std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
829 // std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
830 // std::cout << IndexMap[j].prevResi->info->nr;
831 // std::cout << *(IndexMap[j].prevResi->info->name) ;
832 // std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
833 // std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
834 // std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
835 // std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
836 // std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
842 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
845 switch(initParams.NBS){
846 case (NBSearchMethod::Classique): {
848 // store positions of CA atoms to use them for nbSearch
849 std::vector<gmx::RVec> positionsCA_;
850 for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
852 positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
855 AnalysisNeighborhood nb_;
856 nb_.setCutoff(initParams.cutoff_);
857 AnalysisNeighborhoodPositions nbPos_(positionsCA_);
858 gmx::AnalysisNeighborhoodSearch start = nb_.initSearch(pbc, nbPos_);
859 gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
860 gmx::AnalysisNeighborhoodPair pair;
861 while (pairSearch.findNextPair(&pair))
863 if(CalculateAtomicDistances(
864 IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
865 < minimalCAdistance){
866 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
867 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
868 calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
875 case (NBSearchMethod::Experimental): { // TODO FIX
877 alternateNeighborhoodSearch as_;
879 as_.setCutoff(initParams.cutoff_);
881 as_.AltPairSearch(fr, IndexMap);
883 while (as_.findNextPair()){
884 if(CalculateAtomicDistances(
885 IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
886 < minimalCAdistance){
887 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
888 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
889 calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
898 for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
899 for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
900 if(CalculateAtomicDistances(
901 Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
902 < minimalCAdistance){
903 calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
904 if (Acceptor != Donor + 1){
905 calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
915 // for(std::size_t i {0}; i < IndexMap.size(); ++i){
916 // std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
919 PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
920 calculateBends(fr, pbc);
921 Storage.storageData(frnr, PatternSearch.patternSearch());
925 std::vector<std::pair<int, std::string>> DsspTool::getData(){
926 return Storage.returnData();
929 } // namespace analysismodules