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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 ){
133 // std::cout << "Comparing DONOR " << Donor << " And ACCEPTOR " << Acceptor << " :";
134 // std::cout << "DONOR's acceptor adresses are " << (*ResInfoMap)[Donor].acceptor[0] << ", " << (*ResInfoMap)[Donor].acceptor[1] << " and ACCEPTOR adress is " << (*ResInfoMap)[Acceptor].info << std::endl;
135 // 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;
136 // 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;
138 // if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
139 // ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
140 // std::cout << "HBond Exist" << std::endl;
142 return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
143 ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
147 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
148 std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
154 if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
155 std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
162 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
163 if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
164 return bridgeTypes::None;
166 if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
167 if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
168 return bridgeTypes::ParallelBridge;
170 else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
171 return bridgeTypes::AntiParallelBridge;
174 return bridgeTypes::None;
177 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
178 for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
179 for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
180 bridgeTypes type {calculateBridge(i, j)};
181 if (type == bridgeTypes::None){
199 // for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
200 // for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
201 // if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
202 // if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1]) ||
203 // (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
204 // Bridge[i].push_back(j);
206 // if ((HBondsMap[i][j] && HBondsMap[j][i]) ||
207 // (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
208 // AntiBridge[i].push_back(j);
213 // for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
214 // if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
215 // setStatus(i, secondaryStructureTypes::Bulge);
218 // for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
219 // for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
224 // for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
225 // if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
226 // for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
227 // for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
228 // if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
229 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
230 // && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
231 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
234 // for (std::size_t k{ 0 }; k <= i - j; ++k){
235 // setStatus(i + k, secondaryStructureTypes::Ladder);
239 // for (std::size_t k{ 0 }; k <= j - i; ++k){
240 // setStatus(i + k, secondaryStructureTypes::Ladder);
253 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
254 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
255 std::cout << "Testing Helix_" << static_cast<std::size_t>(i) + 3 << std::endl;
256 std::size_t stride {static_cast<std::size_t>(i) + 3};
257 for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
258 std::cout << "Testing " << j << " and " << j + stride << std::endl;
259 if ( hasHBondBetween(j, j + stride) && NoChainBreaksBetween(j, j + stride) ){
260 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
261 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
263 for (std::size_t k {1}; k < stride; ++k){
264 if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
265 SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
270 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
271 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
274 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
280 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
281 std::size_t stride {static_cast<std::size_t>(i) + 3};
282 for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
283 if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
284 (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
286 secondaryStructureTypes Helix;
288 case turnsTypes::Turn_3:
289 for (std::size_t k {0}; empty && k < stride; ++k){
290 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
292 Helix = secondaryStructureTypes::Helix_3;
294 case turnsTypes::Turn_5:
295 for (std::size_t k {0}; empty && k < stride; ++k){
296 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
298 Helix = secondaryStructureTypes::Helix_5;
301 Helix = secondaryStructureTypes::Helix_4;
304 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
305 for(std::size_t k {0}; k < stride - 1; ++k ){
306 SecondaryStructuresStatusMap[j + k].setStatus(Helix);
313 for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
314 if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
316 for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
317 std::size_t stride {static_cast<std::size_t>(i) + 3};
318 for(std::size_t k {1}; k < stride; ++k){
319 isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
324 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
326 else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
327 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
334 void secondaryStructures::analyzePPHelicesPatterns(){}
336 std::string secondaryStructures::patternSearch(){
339 // analyzeBridgesAndLaddersPatterns();
340 analyzeTurnsAndHelicesPatterns();
341 // analyzePPHelicesPatterns();
342 NoChainBreaksBetween(80, 75);
344 // for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
345 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
348 // std::cout.precision(5);
349 // for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
350 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
351 // if ( (*ResInfoMap)[i].donor[0] != nullptr ){
352 // std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
355 // std::cout << " has no donor[0] and" ;
357 // if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
358 // std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
361 // std::cout << " has no acceptor[0]" ;
363 // std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
364 // if ( (*ResInfoMap)[i].donor[1] != nullptr ){
365 // std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
368 // std::cout << " has no donor[1] and" ;
370 // if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
371 // std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
374 // std::cout << " has no acceptor[1]" ;
380 for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
381 for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
382 if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
383 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
390 if(SecondaryStructuresStatusMap.size() > 1){
391 for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
392 if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
393 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
394 SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
400 return SecondaryStructuresStringLine;
403 secondaryStructures::~secondaryStructures(){
404 SecondaryStructuresStatusMap.resize(0);
405 SecondaryStructuresStringLine.resize(0);
408 DsspTool::DsspStorage::DsspStorage(){
409 storaged_data.resize(0);
412 void DsspTool::DsspStorage::clearAll(){
413 storaged_data.resize(0);
416 std::mutex DsspTool::DsspStorage::mx;
418 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
419 std::lock_guard<std::mutex> guardian(mx);
420 std::pair<int, std::string> datapair(frnr, data);
421 storaged_data.push_back(datapair);
424 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
425 std::sort(storaged_data.begin(), storaged_data.end());
426 return storaged_data;
429 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
430 cutoff = cutoff_init;
433 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
434 while (coordinate < 0) {
435 coordinate += vector_length;
437 while (coordinate >= vector_length) {
438 coordinate -= vector_length;
442 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
451 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
452 rvec coordinates, box_vector_length;
453 num_of_miniboxes.resize(0);
454 num_of_miniboxes.resize(3);
455 for (std::size_t i{XX}; i <= ZZ; ++i) {
456 box_vector_length[i] = std::sqrt(
457 std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
458 num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
460 MiniBoxesMap.resize(0);
461 MiniBoxesReverseMap.resize(0);
462 MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
463 num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
464 num_of_miniboxes[ZZ], std::vector<std::size_t>(
466 MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
467 for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
468 for (std::size_t j{XX}; j <= ZZ; ++j) {
469 coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
470 FixAtomCoordinates(coordinates[j], box_vector_length[j]);
472 MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
473 coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
474 for (std::size_t j{XX}; j <= ZZ; ++j){
475 MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
480 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
481 GetMiniBoxesMap(fr, IndexMap);
482 MiniBoxSize[XX] = MiniBoxesMap.size();
483 MiniBoxSize[YY] = MiniBoxesMap.front().size();
484 MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
486 PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
487 ResiI = PairMap.begin();
488 ResiJ = ResiI->begin();
490 for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
491 for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
492 for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
493 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
494 for (std::size_t k{XX}; k <= ZZ; ++k) {
495 fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
496 ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
498 for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
499 if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
500 PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
501 PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
510 bool alternateNeighborhoodSearch::findNextPair(){
516 for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
517 for(; ResiJ != ResiI->end(); ++ResiJ){
519 resiIpos = ResiI - PairMap.begin();
520 resiJpos = ResiJ - ResiI->begin();
521 if ( ResiJ != ResiI->end() ){
524 else if (ResiI != PairMap.end()) {
526 ResiJ = ResiI->begin();
539 std::size_t alternateNeighborhoodSearch::getResiI() const {
543 std::size_t alternateNeighborhoodSearch::getResiJ() const {
548 DsspTool::DsspStorage DsspTool::Storage;
550 DsspTool::DsspTool(){
553 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
555 const float benddegree{ 70.0 }, maxdist{ 2.5 };
556 float degree{ 0 }, vdist{ 0 }, vprod{ 0 };
557 gmx::RVec a{ 0, 0, 0 }, b{ 0, 0, 0 };
558 for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
560 if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
561 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
566 PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
567 PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
569 // std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
572 for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
574 if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
575 PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
576 PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
577 PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
582 for (int j{ 0 }; j < 3; ++j)
584 a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
585 - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
586 b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
587 - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
589 vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
590 vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
591 IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
594 * gmx::c_angstrom / gmx::c_nano
595 * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
596 IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
599 * gmx::c_angstrom / gmx::c_nano;
600 degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
601 if (degree > benddegree)
603 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
608 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
610 const t_trxframe& fr,
614 * DSSP uses eq from dssp 2.x
615 * kCouplingConstant = 27.888, // = 332 * 0.42 * 0.2
616 * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
621 const float kCouplingConstant = 27.888;
622 const float minimalAtomDistance{ 0.5 },
624 float HbondEnergy{ 0 };
625 float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
627 if( !(Donor.is_proline) ){
628 if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
629 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) ) // Kinda ew
632 distanceNO = CalculateAtomicDistances(
633 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
634 distanceNC = CalculateAtomicDistances(
635 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
637 if (initParams.addHydrogens){
638 if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
639 // std::cout << "On donor " << Donor.info->nr << *(Donor.info->name) << std::endl;
640 // std::cout << "Prev donor is " << Donor.prevResi->info->nr << *(Donor.prevResi->info->name) << std::endl;
641 // std::cout << "Prev C index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomC) << std::endl;
642 // std::cout << "Prev O index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomO) << std::endl;
644 float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
645 for (int i{XX}; i <= ZZ; ++i){
646 float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
647 atomH[i] = prevCO / prevCODist;
649 distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
650 distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
653 distanceHO = distanceNO;
654 distanceHC = distanceNC;
658 distanceHO = CalculateAtomicDistances(
659 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
660 distanceHC = CalculateAtomicDistances(
661 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
664 if (CalculateAtomicDistances(
665 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
668 if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
669 || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
671 HbondEnergy = minEnergy;
673 // std::cout << "HBOND exists cause of distance" << std::endl;
679 * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
680 HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
682 // std::cout.precision(5);
683 // std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
685 // if ( HbondEnergy == 0){
686 // std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
689 if ( HbondEnergy < minEnergy ){
690 HbondEnergy = minEnergy;
697 // std::cerr << "PRO DETECTED! THIS IS RESI № " << Donor.info->nr << std::endl; //IT WORKS JUST FINE
700 if (HbondEnergy < Donor.acceptorEnergy[0]){
701 Donor.acceptor[1] = Donor.acceptor[0];
702 Donor.acceptor[0] = Acceptor.info;
703 Donor.acceptorEnergy[0] = HbondEnergy;
705 else if (HbondEnergy < Donor.acceptorEnergy[1]){
706 Donor.acceptor[1] = Acceptor.info;
707 Donor.acceptorEnergy[1] = HbondEnergy;
710 if (HbondEnergy < Acceptor.donorEnergy[0]){
711 Acceptor.donor[1] = Acceptor.donor[0];
712 Acceptor.donor[0] = Donor.info;
713 Acceptor.donorEnergy[0] = HbondEnergy;
715 else if (HbondEnergy < Acceptor.donorEnergy[1]){
716 Acceptor.donor[1] = Donor.info;
717 Acceptor.donorEnergy[1] = HbondEnergy;
722 /* Calculate Distance From B to A */
723 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
725 gmx::RVec r{ 0, 0, 0 };
726 pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
727 // return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
728 return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
731 /* Calculate Distance From B to A, where A is only fake coordinates */
732 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
734 gmx::RVec r{ 0, 0, 0 };
735 pbc_dx(pbc, A, fr.x[B], r.as_vec());
736 // return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
737 return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
740 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
743 std::cout << "Init started" << std::endl;
744 initParams = initParamz;
745 ResInfo _backboneAtoms;
748 int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
750 IndexMap.push_back(_backboneAtoms);
751 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
752 proLINE = *(IndexMap[i].info->name);
753 if( proLINE.compare("PRO") == 0 ){
754 IndexMap[i].is_proline = true;
757 for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
758 if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
761 resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
762 IndexMap.emplace_back(_backboneAtoms);
763 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
764 proLINE = *(IndexMap[i].info->name);
765 if( proLINE.compare("PRO") == 0 ){
766 IndexMap[i].is_proline = true;
770 std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
771 if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
773 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
775 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
777 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
779 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
781 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
783 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
785 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
787 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
789 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
792 // if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
793 // || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
794 // std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
798 for (std::size_t j {1}; j < IndexMap.size(); ++j){
799 IndexMap[j].prevResi = &(IndexMap[j - 1]);
801 IndexMap[j - 1].nextResi = &(IndexMap[j]);
803 // std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
804 // std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
805 // std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
806 // std::cout << IndexMap[j].prevResi->info->nr;
807 // std::cout << *(IndexMap[j].prevResi->info->name) ;
808 // std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
809 // std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
810 // std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
811 // std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
812 // std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
818 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
821 switch(initParams.NBS){
822 case (NBSearchMethod::Classique): {
824 // store positions of CA atoms to use them for nbSearch
825 std::vector<gmx::RVec> positionsCA_;
826 for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
828 positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
831 AnalysisNeighborhood nb_;
832 nb_.setCutoff(initParams.cutoff_);
833 AnalysisNeighborhoodPositions nbPos_(positionsCA_);
834 gmx::AnalysisNeighborhoodSearch start = nb_.initSearch(pbc, nbPos_);
835 gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
836 gmx::AnalysisNeighborhoodPair pair;
837 while (pairSearch.findNextPair(&pair))
839 if(CalculateAtomicDistances(
840 IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
841 < minimalCAdistance){
842 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
843 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
844 calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
851 case (NBSearchMethod::Experimental): { // TODO FIX
853 alternateNeighborhoodSearch as_;
855 as_.setCutoff(initParams.cutoff_);
857 as_.AltPairSearch(fr, IndexMap);
859 while (as_.findNextPair()){
860 if(CalculateAtomicDistances(
861 IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
862 < minimalCAdistance){
863 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
864 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
865 calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
874 for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
875 for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
876 if(CalculateAtomicDistances(
877 Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
878 < minimalCAdistance){
879 calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
880 if (Acceptor != Donor + 1){
881 calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
891 // for(std::size_t i {0}; i < IndexMap.size(); ++i){
892 // std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
895 PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
896 calculateBends(fr, pbc);
897 Storage.storageData(frnr, PatternSearch.patternSearch());
901 std::vector<std::pair<int, std::string>> DsspTool::getData(){
902 return Storage.returnData();
905 } // namespace analysismodules