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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{
149 std::size_t i{Resi1}, j[Resi2]; // From i to j
155 flag = !(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]));
159 std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
164 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
165 if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
166 return bridgeTypes::None;
168 if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
169 if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
170 return bridgeTypes::ParallelBridge;
172 else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
173 return bridgeTypes::AntiParallelBridge;
176 return bridgeTypes::None;
179 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
180 for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
181 for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
182 bridgeTypes type {calculateBridge(i, j)};
183 if (type == bridgeTypes::None){
201 // for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
202 // for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
203 // if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
204 // if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1]) ||
205 // (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
206 // Bridge[i].push_back(j);
208 // if ((HBondsMap[i][j] && HBondsMap[j][i]) ||
209 // (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
210 // AntiBridge[i].push_back(j);
215 // for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
216 // if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
217 // setStatus(i, secondaryStructureTypes::Bulge);
220 // for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
221 // for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
226 // for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
227 // if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
228 // for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
229 // for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
230 // if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
231 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
232 // && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
233 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
236 // for (std::size_t k{ 0 }; k <= i - j; ++k){
237 // setStatus(i + k, secondaryStructureTypes::Ladder);
241 // for (std::size_t k{ 0 }; k <= j - i; ++k){
242 // setStatus(i + k, secondaryStructureTypes::Ladder);
255 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
256 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
257 std::cout << "Testing Helix_" << static_cast<std::size_t>(i) + 3 << std::endl;
258 std::size_t stride {static_cast<std::size_t>(i) + 3};
259 for(std::size_t j {0}; j + static_cast<std::size_t>(i) < SecondaryStructuresStatusMap.size(); ++j){
260 std::cout << "Testing " << j << " and " << j + stride << std::endl;
261 if ( hasHBondBetween(j, j + (static_cast<std::size_t>(i))) && NoChainBreaksBetween(j, j + stride) ){
262 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
263 SecondaryStructuresStatusMap[j + static_cast<std::size_t>(i)].setStatus(HelixPositions::End, i);
265 for (std::size_t k {1}; k < (static_cast<std::size_t>(i)); ++k){
266 if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
267 SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
272 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
273 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
276 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
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 for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
285 if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
286 (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
288 secondaryStructureTypes Helix;
290 case turnsTypes::Turn_3:
291 for (std::size_t k {0}; empty && k < stride; ++k){
292 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
294 Helix = secondaryStructureTypes::Helix_3;
296 case turnsTypes::Turn_5:
297 for (std::size_t k {0}; empty && k < stride; ++k){
298 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5));
300 Helix = secondaryStructureTypes::Helix_4;
303 Helix = secondaryStructureTypes::Helix_4;
306 std::cout << j << " is HELIX" << std::endl;
308 for(std::size_t k {0}; k < (static_cast<std::size_t>(i)); ++k ){
309 SecondaryStructuresStatusMap[j + k].setStatus(Helix);
316 for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
317 if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
319 for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
320 std::size_t stride {static_cast<std::size_t>(i) + 3};
321 for(std::size_t k {1}; k < stride; ++k){
322 isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
327 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
329 else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
330 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
337 void secondaryStructures::analyzePPHelicesPatterns(){}
339 std::string secondaryStructures::patternSearch(){
341 // analyzeBridgesAndLaddersPatterns();
342 analyzeTurnsAndHelicesPatterns();
343 // analyzePPHelicesPatterns();
345 // for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
346 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
349 // std::cout.precision(5);
350 // for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
351 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
352 // if ( (*ResInfoMap)[i].donor[0] != nullptr ){
353 // std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
356 // std::cout << " has no donor[0] and" ;
358 // if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
359 // std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
362 // std::cout << " has no acceptor[0]" ;
364 // std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
365 // if ( (*ResInfoMap)[i].donor[1] != nullptr ){
366 // std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
369 // std::cout << " has no donor[1] and" ;
371 // if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
372 // std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
375 // std::cout << " has no acceptor[1]" ;
381 for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
382 for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
383 if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
384 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
391 if(SecondaryStructuresStatusMap.size() > 1){
392 for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
393 if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
394 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
395 SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
401 return SecondaryStructuresStringLine;
404 secondaryStructures::~secondaryStructures(){
405 SecondaryStructuresStatusMap.resize(0);
406 SecondaryStructuresStringLine.resize(0);
409 DsspTool::DsspStorage::DsspStorage(){
410 storaged_data.resize(0);
413 void DsspTool::DsspStorage::clearAll(){
414 storaged_data.resize(0);
417 std::mutex DsspTool::DsspStorage::mx;
419 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
420 std::lock_guard<std::mutex> guardian(mx);
421 std::pair<int, std::string> datapair(frnr, data);
422 storaged_data.push_back(datapair);
425 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
426 std::sort(storaged_data.begin(), storaged_data.end());
427 return storaged_data;
430 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
431 cutoff = cutoff_init;
434 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
435 while (coordinate < 0) {
436 coordinate += vector_length;
438 while (coordinate >= vector_length) {
439 coordinate -= vector_length;
443 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
452 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
453 rvec coordinates, box_vector_length;
454 num_of_miniboxes.resize(0);
455 num_of_miniboxes.resize(3);
456 for (std::size_t i{XX}; i <= ZZ; ++i) {
457 box_vector_length[i] = std::sqrt(
458 std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
459 num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
461 MiniBoxesMap.resize(0);
462 MiniBoxesReverseMap.resize(0);
463 MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
464 num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
465 num_of_miniboxes[ZZ], std::vector<std::size_t>(
467 MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
468 for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
469 for (std::size_t j{XX}; j <= ZZ; ++j) {
470 coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
471 FixAtomCoordinates(coordinates[j], box_vector_length[j]);
473 MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
474 coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
475 for (std::size_t j{XX}; j <= ZZ; ++j){
476 MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
481 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
482 GetMiniBoxesMap(fr, IndexMap);
483 MiniBoxSize[XX] = MiniBoxesMap.size();
484 MiniBoxSize[YY] = MiniBoxesMap.front().size();
485 MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
487 PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
488 ResiI = PairMap.begin();
489 ResiJ = ResiI->begin();
491 for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
492 for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
493 for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
494 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
495 for (std::size_t k{XX}; k <= ZZ; ++k) {
496 fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
497 ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
499 for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
500 if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
501 PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
502 PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
511 bool alternateNeighborhoodSearch::findNextPair(){
517 for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
518 for(; ResiJ != ResiI->end(); ++ResiJ){
520 resiIpos = ResiI - PairMap.begin();
521 resiJpos = ResiJ - ResiI->begin();
522 if ( ResiJ != ResiI->end() ){
525 else if (ResiI != PairMap.end()) {
527 ResiJ = ResiI->begin();
540 std::size_t alternateNeighborhoodSearch::getResiI() const {
544 std::size_t alternateNeighborhoodSearch::getResiJ() const {
549 DsspTool::DsspStorage DsspTool::Storage;
551 DsspTool::DsspTool(){
554 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
556 const float benddegree{ 70.0 }, maxdist{ 2.5 };
557 float degree{ 0 }, vdist{ 0 }, vprod{ 0 };
558 gmx::RVec a{ 0, 0, 0 }, b{ 0, 0, 0 };
559 for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
561 if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
562 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
567 PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
568 PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
570 // std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
573 for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
575 if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
576 PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
577 PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
578 PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
583 for (int j{ 0 }; j < 3; ++j)
585 a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
586 - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
587 b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
588 - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
590 vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
591 vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
592 IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
595 * gmx::c_angstrom / gmx::c_nano
596 * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
597 IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
600 * gmx::c_angstrom / gmx::c_nano;
601 degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
602 if (degree > benddegree)
604 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
609 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
611 const t_trxframe& fr,
615 * DSSP uses eq from dssp 2.x
616 * kCouplingConstant = 27.888, // = 332 * 0.42 * 0.2
617 * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
622 const float kCouplingConstant = 27.888;
623 const float minimalAtomDistance{ 0.5 },
625 float HbondEnergy{ 0 };
626 float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
628 if( !(Donor.is_proline) ){
629 if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
630 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) ) // Kinda ew
633 distanceNO = CalculateAtomicDistances(
634 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
635 distanceNC = CalculateAtomicDistances(
636 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
638 if (initParams.addHydrogens){
639 if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
640 // std::cout << "On donor " << Donor.info->nr << *(Donor.info->name) << std::endl;
641 // std::cout << "Prev donor is " << Donor.prevResi->info->nr << *(Donor.prevResi->info->name) << std::endl;
642 // std::cout << "Prev C index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomC) << std::endl;
643 // std::cout << "Prev O index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomO) << std::endl;
645 float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
646 for (int i{XX}; i <= ZZ; ++i){
647 float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
648 atomH[i] = prevCO / prevCODist;
650 distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
651 distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
654 distanceHO = distanceNO;
655 distanceHC = distanceNC;
659 distanceHO = CalculateAtomicDistances(
660 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
661 distanceHC = CalculateAtomicDistances(
662 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
665 if (CalculateAtomicDistances(
666 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
669 if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
670 || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
672 HbondEnergy = minEnergy;
674 // std::cout << "HBOND exists cause of distance" << std::endl;
680 * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
681 HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
683 // std::cout.precision(5);
684 // std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
686 // if ( HbondEnergy == 0){
687 // std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
690 if ( HbondEnergy < minEnergy ){
691 HbondEnergy = minEnergy;
698 // std::cerr << "PRO DETECTED! THIS IS RESI № " << Donor.info->nr << std::endl; //IT WORKS JUST FINE
701 if (HbondEnergy < Donor.acceptorEnergy[0]){
702 Donor.acceptor[1] = Donor.acceptor[0];
703 Donor.acceptor[0] = Acceptor.info;
704 Donor.acceptorEnergy[0] = HbondEnergy;
706 else if (HbondEnergy < Donor.acceptorEnergy[1]){
707 Donor.acceptor[1] = Acceptor.info;
708 Donor.acceptorEnergy[1] = HbondEnergy;
711 if (HbondEnergy < Acceptor.donorEnergy[0]){
712 Acceptor.donor[1] = Acceptor.donor[0];
713 Acceptor.donor[0] = Donor.info;
714 Acceptor.donorEnergy[0] = HbondEnergy;
716 else if (HbondEnergy < Acceptor.donorEnergy[1]){
717 Acceptor.donor[1] = Donor.info;
718 Acceptor.donorEnergy[1] = HbondEnergy;
723 /* Calculate Distance From B to A */
724 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
726 gmx::RVec r{ 0, 0, 0 };
727 pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
728 // return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
729 return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
732 /* Calculate Distance From B to A, where A is only fake coordinates */
733 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
735 gmx::RVec r{ 0, 0, 0 };
736 pbc_dx(pbc, A, fr.x[B], r.as_vec());
737 // return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
738 return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
741 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
744 std::cout << "Init started" << std::endl;
745 initParams = initParamz;
746 ResInfo _backboneAtoms;
749 int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
751 IndexMap.push_back(_backboneAtoms);
752 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
753 proLINE = *(IndexMap[i].info->name);
754 if( proLINE.compare("PRO") == 0 ){
755 IndexMap[i].is_proline = true;
758 for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
759 if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
762 resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
763 IndexMap.emplace_back(_backboneAtoms);
764 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
765 proLINE = *(IndexMap[i].info->name);
766 if( proLINE.compare("PRO") == 0 ){
767 IndexMap[i].is_proline = true;
771 std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
772 if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
774 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
776 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
778 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
780 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
782 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
784 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
786 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
788 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
790 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
793 // if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
794 // || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
795 // std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
799 for (std::size_t j {1}; j < IndexMap.size(); ++j){
800 IndexMap[j].prevResi = &(IndexMap[j - 1]);
802 IndexMap[j - 1].nextResi = &(IndexMap[j]);
804 // std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
805 // std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
806 // std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
807 // std::cout << IndexMap[j].prevResi->info->nr;
808 // std::cout << *(IndexMap[j].prevResi->info->name) ;
809 // std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
810 // std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
811 // std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
812 // std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
813 // std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
819 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
822 switch(initParams.NBS){
823 case (NBSearchMethod::Classique): {
825 // store positions of CA atoms to use them for nbSearch
826 std::vector<gmx::RVec> positionsCA_;
827 for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
829 positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
832 AnalysisNeighborhood nb_;
833 nb_.setCutoff(initParams.cutoff_);
834 AnalysisNeighborhoodPositions nbPos_(positionsCA_);
835 gmx::AnalysisNeighborhoodSearch start = nb_.initSearch(pbc, nbPos_);
836 gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
837 gmx::AnalysisNeighborhoodPair pair;
838 while (pairSearch.findNextPair(&pair))
840 if(CalculateAtomicDistances(
841 IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
842 < minimalCAdistance){
843 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
844 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
845 calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
852 case (NBSearchMethod::Experimental): { // TODO FIX
854 alternateNeighborhoodSearch as_;
856 as_.setCutoff(initParams.cutoff_);
858 as_.AltPairSearch(fr, IndexMap);
860 while (as_.findNextPair()){
861 if(CalculateAtomicDistances(
862 IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
863 < minimalCAdistance){
864 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
865 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
866 calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
875 for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
876 for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
877 if(CalculateAtomicDistances(
878 Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
879 < minimalCAdistance){
880 calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
881 if (Acceptor != Donor + 1){
882 calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
892 // for(std::size_t i {0}; i < IndexMap.size(); ++i){
893 // std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
896 PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
897 calculateBends(fr, pbc);
898 Storage.storageData(frnr, PatternSearch.patternSearch());
902 std::vector<std::pair<int, std::string>> DsspTool::getData(){
903 return Storage.returnData();
906 } // namespace analysismodules