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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 of the last residue
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{ // prob should add resi name comparison ?
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;
144 // std::cout << "Comparing DONOR " << Donor << " And ACCEPTOR " << Acceptor << ": ";
145 // std::cout << "DONOR's acceptor adresses are " << (*ResInfoMap)[Donor].acceptor[0] << ", " << (*ResInfoMap)[Donor].acceptor[1] << " and ACCEPTOR adress is " << (*ResInfoMap)[Acceptor].info << std::endl;
146 // std::cout << "DONOR's acceptors' nr are = " << (*ResInfoMap)[Donor].acceptor[0]->nr << ", " << (*ResInfoMap)[Donor].acceptor[1]->nr << " And ACCEPTOR's nr = " << (*ResInfoMap)[Acceptor].info->nr << std::endl;
147 // std::cout << "DONOR's acceptors' chainID are = " << (*ResInfoMap)[Donor].acceptor[0]->chainid << ", " << (*ResInfoMap)[Donor].acceptor[1]->chainid << " And ACCEPTOR's chainID = " << (*ResInfoMap)[Acceptor].info->chainid << std::endl;
149 // if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
150 // ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
151 // std::cout << "HBond Exist" << std::endl;
159 return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
160 ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
165 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
166 std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
172 if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
173 std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
180 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
181 if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
182 return bridgeTypes::None;
184 if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
185 if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
186 return bridgeTypes::ParallelBridge;
188 else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
189 return bridgeTypes::AntiParallelBridge;
192 return bridgeTypes::None;
195 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
196 for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
197 for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
198 bridgeTypes type {calculateBridge(i, j)};
199 if (type == bridgeTypes::None){
217 // for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
218 // for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
219 // if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
220 // if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1]) ||
221 // (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
222 // Bridge[i].push_back(j);
224 // if ((HBondsMap[i][j] && HBondsMap[j][i]) ||
225 // (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
226 // AntiBridge[i].push_back(j);
231 // for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
232 // if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
233 // setStatus(i, secondaryStructureTypes::Bulge);
236 // for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
237 // for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
242 // for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
243 // if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
244 // for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
245 // for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
246 // if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
247 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
248 // && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
249 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
252 // for (std::size_t k{ 0 }; k <= i - j; ++k){
253 // setStatus(i + k, secondaryStructureTypes::Ladder);
257 // for (std::size_t k{ 0 }; k <= j - i; ++k){
258 // setStatus(i + k, secondaryStructureTypes::Ladder);
271 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
272 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
273 std::size_t stride {static_cast<std::size_t>(i) + 3};
274 std::cout << "Testing Helix_" << stride << std::endl;
275 for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
276 std::cout << "Testing " << j << " and " << j + stride << std::endl;
277 if ( hasHBondBetween(j, j + stride) && NoChainBreaksBetween(j, j + stride) ){
278 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
279 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
281 for (std::size_t k {1}; k < stride; ++k){
282 if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
283 SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
284 SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
289 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
290 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
293 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
299 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
300 std::size_t stride {static_cast<std::size_t>(i) + 3};
301 for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
302 if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
303 (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
305 secondaryStructureTypes Helix;
307 case turnsTypes::Turn_3:
308 for (std::size_t k {0}; empty && k < stride; ++k){
309 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
311 Helix = secondaryStructureTypes::Helix_3;
313 case turnsTypes::Turn_5:
314 for (std::size_t k {0}; empty && k < stride; ++k){
315 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
317 Helix = secondaryStructureTypes::Helix_5;
320 Helix = secondaryStructureTypes::Helix_4;
323 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
324 for(std::size_t k {0}; k < stride - 1; ++k ){
325 SecondaryStructuresStatusMap[j + k].setStatus(Helix);
332 // for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
333 // if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
334 // bool isTurn = false;
335 // for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
336 // std::size_t stride {static_cast<std::size_t>(i) + 3};
337 // for(std::size_t k {1}; k < stride; ++k){
338 // isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
343 // SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
345 // else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
346 // SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
353 void secondaryStructures::analyzePPHelicesPatterns(){}
355 std::string secondaryStructures::patternSearch(){
358 // analyzeBridgesAndLaddersPatterns();
359 analyzeTurnsAndHelicesPatterns();
360 // analyzePPHelicesPatterns();
362 // for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
363 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
366 // std::cout.precision(5);
367 // for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
368 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
369 // if ( (*ResInfoMap)[i].donor[0] != nullptr ){
370 // std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
373 // std::cout << " has no donor[0] and" ;
375 // if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
376 // std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
379 // std::cout << " has no acceptor[0]" ;
381 // std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
382 // if ( (*ResInfoMap)[i].donor[1] != nullptr ){
383 // std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
386 // std::cout << " has no donor[1] and" ;
388 // if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
389 // std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
392 // std::cout << " has no acceptor[1]" ;
398 for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
399 for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
400 if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
401 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
408 if(SecondaryStructuresStatusMap.size() > 1){
409 for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
410 if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
411 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
412 SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
418 return SecondaryStructuresStringLine;
421 secondaryStructures::~secondaryStructures(){
422 SecondaryStructuresStatusMap.resize(0);
423 SecondaryStructuresStringLine.resize(0);
426 DsspTool::DsspStorage::DsspStorage(){
427 storaged_data.resize(0);
430 void DsspTool::DsspStorage::clearAll(){
431 storaged_data.resize(0);
434 std::mutex DsspTool::DsspStorage::mx;
436 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
437 std::lock_guard<std::mutex> guardian(mx);
438 std::pair<int, std::string> datapair(frnr, data);
439 storaged_data.push_back(datapair);
442 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
443 std::sort(storaged_data.begin(), storaged_data.end());
444 return storaged_data;
447 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
448 cutoff = cutoff_init;
451 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
452 while (coordinate < 0) {
453 coordinate += vector_length;
455 while (coordinate >= vector_length) {
456 coordinate -= vector_length;
460 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
469 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
470 rvec coordinates, box_vector_length;
471 num_of_miniboxes.resize(0);
472 num_of_miniboxes.resize(3);
473 for (std::size_t i{XX}; i <= ZZ; ++i) {
474 box_vector_length[i] = std::sqrt(
475 std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
476 num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
478 MiniBoxesMap.resize(0);
479 MiniBoxesReverseMap.resize(0);
480 MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
481 num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
482 num_of_miniboxes[ZZ], std::vector<std::size_t>(
484 MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
485 for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
486 for (std::size_t j{XX}; j <= ZZ; ++j) {
487 coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
488 FixAtomCoordinates(coordinates[j], box_vector_length[j]);
490 MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
491 coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
492 for (std::size_t j{XX}; j <= ZZ; ++j){
493 MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
498 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
499 GetMiniBoxesMap(fr, IndexMap);
500 MiniBoxSize[XX] = MiniBoxesMap.size();
501 MiniBoxSize[YY] = MiniBoxesMap.front().size();
502 MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
504 PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
505 ResiI = PairMap.begin();
506 ResiJ = ResiI->begin();
508 for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
509 for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
510 for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
511 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
512 for (std::size_t k{XX}; k <= ZZ; ++k) {
513 fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
514 ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
516 for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
517 if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
518 PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
519 PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
528 bool alternateNeighborhoodSearch::findNextPair(){
534 for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
535 for(; ResiJ != ResiI->end(); ++ResiJ){
537 resiIpos = ResiI - PairMap.begin();
538 resiJpos = ResiJ - ResiI->begin();
539 if ( ResiJ != ResiI->end() ){
542 else if (ResiI != PairMap.end()) {
544 ResiJ = ResiI->begin();
557 std::size_t alternateNeighborhoodSearch::getResiI() const {
561 std::size_t alternateNeighborhoodSearch::getResiJ() const {
566 DsspTool::DsspStorage DsspTool::Storage;
568 DsspTool::DsspTool(){
571 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
573 const float benddegree{ 70.0 }, maxdist{ 2.5 };
574 float degree{ 0 }, vdist{ 0 }, vprod{ 0 };
575 gmx::RVec a{ 0, 0, 0 }, b{ 0, 0, 0 };
576 for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
578 if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
579 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
584 PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
585 PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
587 // std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
590 for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
592 if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
593 PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
594 PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
595 PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
600 for (int j{ 0 }; j < 3; ++j)
602 a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
603 - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
604 b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
605 - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
607 vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
608 vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
609 IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
612 * gmx::c_angstrom / gmx::c_nano
613 * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
614 IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
617 * gmx::c_angstrom / gmx::c_nano;
618 degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
619 if (degree > benddegree)
621 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
626 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
628 const t_trxframe& fr,
632 * DSSP uses eq from dssp 2.x
633 * kCouplingConstant = 27.888, // = 332 * 0.42 * 0.2
634 * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
638 * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
642 const float kCouplingConstant = 27.888;
643 const float minimalAtomDistance{ 0.5 },
645 float HbondEnergy{ 0 };
646 float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
648 if( !(Donor.is_proline) ){
649 if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
650 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )
653 distanceNO = CalculateAtomicDistances(
654 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
655 distanceNC = CalculateAtomicDistances(
656 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
658 if (initParams.addHydrogens){
659 if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
661 float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
662 for (int i{XX}; i <= ZZ; ++i){
663 float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
664 atomH[i] = prevCO / prevCODist;
666 distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
667 distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
670 distanceHO = distanceNO;
671 distanceHC = distanceNC;
675 distanceHO = CalculateAtomicDistances(
676 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
677 distanceHC = CalculateAtomicDistances(
678 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
681 std::cout << "CA-CA distance: " << CalculateAtomicDistances(
682 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
683 std::cout << "N-O distance: " << distanceNO << std::endl;
684 std::cout << "N-C distance: " << distanceNC << std::endl;
685 std::cout << "H-O distance: " << distanceHO << std::endl;
686 std::cout << "H-C distance: " << distanceHC << std::endl;
688 if (CalculateAtomicDistances(
689 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
692 if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
693 || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
695 HbondEnergy = minEnergy;
701 * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
702 // HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
704 // std::cout.precision(5);
705 // std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
707 // if ( HbondEnergy == 0){
708 // std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
711 if ( HbondEnergy < minEnergy ){
712 HbondEnergy = minEnergy;
719 if (HbondEnergy < Donor.acceptorEnergy[0]){
720 Donor.acceptor[1] = Donor.acceptor[0];
721 Donor.acceptor[0] = Acceptor.info;
722 Donor.acceptorEnergy[0] = HbondEnergy;
724 else if (HbondEnergy < Donor.acceptorEnergy[1]){
725 Donor.acceptor[1] = Acceptor.info;
726 Donor.acceptorEnergy[1] = HbondEnergy;
729 if (HbondEnergy < Acceptor.donorEnergy[0]){
730 Acceptor.donor[1] = Acceptor.donor[0];
731 Acceptor.donor[0] = Donor.info;
732 Acceptor.donorEnergy[0] = HbondEnergy;
734 else if (HbondEnergy < Acceptor.donorEnergy[1]){
735 Acceptor.donor[1] = Donor.info;
736 Acceptor.donorEnergy[1] = HbondEnergy;
741 /* Calculate Distance From B to A */
742 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
744 gmx::RVec r{ 0, 0, 0 };
745 pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
746 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
749 /* Calculate Distance From B to A, where A is only fake coordinates */
750 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
752 gmx::RVec r{ 0, 0, 0 };
753 pbc_dx(pbc, A, fr.x[B], r.as_vec());
754 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
757 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
760 std::cout << "Init started" << std::endl;
761 initParams = initParamz;
762 ResInfo _backboneAtoms;
765 int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
767 IndexMap.push_back(_backboneAtoms);
768 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
769 proLINE = *(IndexMap[i].info->name);
770 if( proLINE.compare("PRO") == 0 ){
771 IndexMap[i].is_proline = true;
774 for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
775 if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
778 resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
779 IndexMap.emplace_back(_backboneAtoms);
780 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
781 proLINE = *(IndexMap[i].info->name);
782 if( proLINE.compare("PRO") == 0 ){
783 IndexMap[i].is_proline = true;
787 std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
788 if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
790 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
792 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
794 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
796 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
798 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
800 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
802 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
803 if (initParamz.addHydrogens == true){
804 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
807 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
809 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
814 // if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
815 // || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
816 // std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
820 for (std::size_t j {1}; j < IndexMap.size(); ++j){
821 IndexMap[j].prevResi = &(IndexMap[j - 1]);
823 IndexMap[j - 1].nextResi = &(IndexMap[j]);
825 // std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
826 // std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
827 // std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
828 // std::cout << IndexMap[j].prevResi->info->nr;
829 // std::cout << *(IndexMap[j].prevResi->info->name) ;
830 // std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
831 // std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
832 // std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
833 // std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
834 // std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
840 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
843 switch(initParams.NBS){
844 case (NBSearchMethod::Classique): {
846 // store positions of CA atoms to use them for nbSearch
847 std::vector<gmx::RVec> positionsCA_;
848 for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
850 positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
853 AnalysisNeighborhood nb_;
854 nb_.setCutoff(initParams.cutoff_);
855 AnalysisNeighborhoodPositions nbPos_(positionsCA_);
856 gmx::AnalysisNeighborhoodSearch start = nb_.initSearch(pbc, nbPos_);
857 gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
858 gmx::AnalysisNeighborhoodPair pair;
859 while (pairSearch.findNextPair(&pair))
861 if(CalculateAtomicDistances(
862 IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
863 < minimalCAdistance){
864 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
865 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
866 calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
873 case (NBSearchMethod::Experimental): { // TODO FIX
875 alternateNeighborhoodSearch as_;
877 as_.setCutoff(initParams.cutoff_);
879 as_.AltPairSearch(fr, IndexMap);
881 while (as_.findNextPair()){
882 if(CalculateAtomicDistances(
883 IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
884 < minimalCAdistance){
885 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
886 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
887 calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
896 for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
897 for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
898 if(CalculateAtomicDistances(
899 Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
900 < minimalCAdistance){
901 calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
902 if (Acceptor != Donor + 1){
903 calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
913 // for(std::size_t i {0}; i < IndexMap.size(); ++i){
914 // std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
917 PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
918 calculateBends(fr, pbc);
919 Storage.storageData(frnr, PatternSearch.patternSearch());
923 std::vector<std::pair<int, std::string>> DsspTool::getData(){
924 return Storage.returnData();
927 } // namespace analysismodules