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37 * Implements gmx::analysismodules::Trajectory.
39 * \author Sergey Gorelov <gorelov_sv@pnpi.nrcki.ru>
40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
41 * \author Alexey Shvetsov <alexxyum@gmail.com>
42 * \ingroup module_trajectoryanalysis
46 There's something wrong with energy calculations of redidues with E ≈ -0
50 #include "dssptools.h"
53 #include "gromacs/math/units.h"
55 #include "gromacs/pbcutil/pbc.h"
56 #include <gromacs/trajectoryanalysis.h>
57 #include "gromacs/trajectoryanalysis/topologyinformation.h"
66 namespace analysismodules
69 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
71 // _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
74 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
76 // return _ResInfo[static_cast<std::size_t>(atomTypeName)];
79 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
80 return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
83 secondaryStructures::secondaryStructures(){
85 void secondaryStructures::initiateSearch(const std::vector<ResInfo> &ResInfoMatrix, const bool PiHelicesPreferencez){
86 SecondaryStructuresStatusMap.resize(0);
87 SecondaryStructuresStringLine.resize(0);
88 std::vector<std::size_t> temp; temp.resize(0),
89 PiHelixPreference = PiHelicesPreferencez;
90 ResInfoMap = &ResInfoMatrix;
91 SecondaryStructuresStatusMap.resize(ResInfoMatrix.size());
92 SecondaryStructuresStringLine.resize(ResInfoMatrix.size(), '~');
95 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName){
96 SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = true;
97 SecondaryStructuresStatus = secondaryStructureTypeName;
100 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
101 TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
104 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
105 return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
108 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
109 return breakPartners[0] == partner || breakPartners[1] == partner;
112 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
113 return TurnsStatusArray[static_cast<std::size_t>(turn)];
116 secondaryStructureTypes secondaryStructures::secondaryStructuresData::getStatus() const{
117 return SecondaryStructuresStatus;
120 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
121 if (breakPartners[0] == nullptr){
122 breakPartners[0] = breakPartner;
125 breakPartners[1] = breakPartner;
127 setStatus(secondaryStructureTypes::Break);
130 void secondaryStructures::secondaryStructuresData::setBridge(secondaryStructuresData *bridgePartner, std::size_t bridgePartnerIndex, bridgeTypes bridgeType){
131 if(bridgeType == bridgeTypes::ParallelBridge){
132 bridgePartners[0] = bridgePartner;
133 bridgePartnersIndexes[0] = bridgePartnerIndex;
135 else if (bridgeType == bridgeTypes::AntiParallelBridge){
136 bridgePartners[1] = bridgePartner;
137 bridgePartnersIndexes[1] = bridgePartnerIndex;
141 bool secondaryStructures::secondaryStructuresData::hasBridges() const{
142 return bridgePartners[0] || bridgePartners[1];
146 bool secondaryStructures::secondaryStructuresData::hasBridges(bridgeTypes bridgeType) const{
147 if(bridgeType == bridgeTypes::ParallelBridge){
148 return bridgePartners[0] != nullptr;
150 else if (bridgeType == bridgeTypes::AntiParallelBridge){
151 return bridgePartners[1] != nullptr;
158 bool secondaryStructures::secondaryStructuresData::isBridgePartnerWith(secondaryStructuresData *bridgePartner, bridgeTypes bridgeType) const{
159 if(bridgeType == bridgeTypes::ParallelBridge){
160 return bridgePartners[0] == bridgePartner;
162 else if (bridgeType == bridgeTypes::AntiParallelBridge){
163 return bridgePartners[1] == bridgePartner;
168 std::size_t secondaryStructures::secondaryStructuresData::getBridgePartnerIndex(bridgeTypes bridgeType) const{
169 if (bridgeType == bridgeTypes::ParallelBridge){
170 return bridgePartnersIndexes[0];
172 return bridgePartnersIndexes[1];
175 secondaryStructures::secondaryStructuresData secondaryStructures::secondaryStructuresData::getBridgePartner(bridgeTypes bridgeType) const{
176 if(bridgeType == bridgeTypes::ParallelBridge){
177 return *(bridgePartners[0]);
179 return *(bridgePartners[1]);
182 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
183 if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
184 (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
185 (*ResInfoMap)[Acceptor].info == nullptr ){
186 // std::cout << "Bad hbond check. Reason(s): " ;
187 // if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
188 // std::cout << "Donor has no acceptor[0]; ";
190 // if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
191 // std::cout << "Donor has no acceptor[1]; ";
193 // if ( (*ResInfoMap)[Acceptor].info == nullptr ){
194 // std::cout << "No info about acceptor; ";
196 // std::cout << std::endl;
199 // else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
200 // (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
201 // (*ResInfoMap)[Donor].info == nullptr )) {
202 // std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
203 // std::cout << "Donor's acceptors' nr are = " << (*ResInfoMap)[Donor].acceptor[0]->nr << " (chain " << (*ResInfoMap)[Donor].acceptor[0]->chainid << ") , " << (*ResInfoMap)[Donor].acceptor[1]->nr << " (chain " << (*ResInfoMap)[Donor].acceptor[1]->chainid << ")" << std::endl;
204 // std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
205 // std::cout << "Acceptors's donors' nr are = " << (*ResInfoMap)[Acceptor].donor[0]->nr << " (chain " << (*ResInfoMap)[Acceptor].donor[0]->chainid << ") , " << (*ResInfoMap)[Acceptor].donor[1]->nr << " (chain " << (*ResInfoMap)[Acceptor].donor[1]->chainid << ")" << std::endl;
206 // std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
207 // if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
208 // ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
209 // std::cout << "HBond Exist" << std::endl;
213 // std::cout << "Bad hbond check. Reason(s): " ;
214 // if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
215 // std::cout << "Acceptor has no donor[0]; ";
217 // if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
218 // std::cout << "Acceptor has no donor[1]; ";
220 // if ( (*ResInfoMap)[Donor].info == nullptr ){
221 // std::cout << "No info about donor; ";
223 // std::cout << std::endl;
226 return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
227 ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
232 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
233 std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
239 if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
240 std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
247 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
248 if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){ // Protection from idiotz, не обязательно нужен
249 return bridgeTypes::None;
252 ResInfo a{(*ResInfoMap)[i]}, b{(*ResInfoMap)[j]};
254 if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1) && a.prevResi && a.nextResi && b.prevResi && b.nextResi){
255 if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){
256 return bridgeTypes::ParallelBridge;
258 else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){
259 return bridgeTypes::AntiParallelBridge;
262 return bridgeTypes::None;
265 void secondaryStructures::analyzeBridgesAndStrandsPatterns(){
267 for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
268 for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
269 switch(calculateBridge(i, j)){
270 case bridgeTypes::ParallelBridge : {
271 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::ParallelBridge);
272 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
273 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::ParallelBridge);
274 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
276 case bridgeTypes::AntiParallelBridge : {
277 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::AntiParallelBridge);
278 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
279 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::AntiParallelBridge);
280 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
287 // Calculate Extended Strandz
288 for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
289 bool is_Estrand {false};
290 for(std::size_t j {2}; j != 0; --j){
291 for(const bridgeTypes &bridgeType : {bridgeTypes::ParallelBridge, bridgeTypes::AntiParallelBridge}){
292 if (SecondaryStructuresStatusMap[i].hasBridges(bridgeType) && SecondaryStructuresStatusMap[i + j].hasBridges(bridgeType) ){
293 std::size_t i_partner{SecondaryStructuresStatusMap[i].getBridgePartnerIndex(bridgeType)}, j_partner{SecondaryStructuresStatusMap[i + j].getBridgePartnerIndex(bridgeType)}, second_strand{};
294 std::cout << "i = " << i << std::endl;
295 std::cout << "j = " << j << std::endl;
296 std::cout << "i_partner = " << i_partner << std::endl;
297 std::cout << "j_partner = " << j_partner << std::endl;
298 if ( abs(i_partner - j_partner) < 6){
299 if (i_partner < j_partner){
300 second_strand = i_partner;
303 second_strand = j_partner;
305 for(int k{abs(i_partner - j_partner)}; k >= 0; --k){
306 SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Strand);
307 std::cout << second_strand + k << " is strand" << std::endl;
316 SecondaryStructuresStatusMap[i + j].setStatus(secondaryStructureTypes::Strand);
317 std::cout << i + j << " is strand" << std::endl;
335 // for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
336 // for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
337 // if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
338 // if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1]) ||
339 // (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
340 // Bridge[i].push_back(j);
342 // if ((HBondsMap[i][j] && HBondsMap[j][i]) ||
343 // (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
344 // AntiBridge[i].push_back(j);
349 // for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
350 // if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
351 // setStatus(i, secondaryStructureTypes::Bulge);
354 // for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
355 // for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
360 // for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
361 // if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
362 // for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
363 // for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
364 // if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
365 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
366 // && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
367 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
370 // for (std::size_t k{ 0 }; k <= i - j; ++k){
371 // setStatus(i + k, secondaryStructureTypes::Ladder);
375 // for (std::size_t k{ 0 }; k <= j - i; ++k){
376 // setStatus(i + k, secondaryStructureTypes::Ladder);
389 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
390 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
391 std::size_t stride {static_cast<std::size_t>(i) + 3};
392 std::cout << "Testing Helix_" << stride << std::endl;
393 for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
394 std::cout << "Testing " << j << " and " << j + stride << std::endl;
395 if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
396 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
397 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
399 for (std::size_t k {1}; k < stride; ++k){
400 if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
401 SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
402 SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
406 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
407 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
410 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
416 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
417 std::size_t stride {static_cast<std::size_t>(i) + 3};
418 for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
419 if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
420 (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
422 secondaryStructureTypes Helix;
424 case turnsTypes::Turn_3:
425 for (std::size_t k {0}; empty && k < stride; ++k){
426 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
428 Helix = secondaryStructureTypes::Helix_3;
430 case turnsTypes::Turn_5:
431 for (std::size_t k {0}; empty && k < stride; ++k){
432 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
434 Helix = secondaryStructureTypes::Helix_5;
437 Helix = secondaryStructureTypes::Helix_4;
440 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
441 for(std::size_t k {0}; k < stride; ++k ){
442 SecondaryStructuresStatusMap[j + k].setStatus(Helix);
449 /* Не знаю зач они в дссп так сделали, этож полное говно */
451 // for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
452 // if (SecondaryStructuresStatusMap[i].getStatus() == secondaryStructureTypes::Loop || SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
453 // bool isTurn = false;
454 // for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
455 // std::size_t stride {static_cast<std::size_t>(j) + 3};
456 // for(std::size_t k {1}; k < stride and !isTurn; ++k){
457 // isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
461 // SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
468 void secondaryStructures::analyzePPHelicesPatterns(){}
470 std::string secondaryStructures::patternSearch(){
473 analyzeBridgesAndStrandsPatterns();
474 analyzeTurnsAndHelicesPatterns();
475 // analyzePPHelicesPatterns();
477 // for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
478 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
481 // std::cout.precision(5);
482 // for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
483 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
484 // if ( (*ResInfoMap)[i].donor[0] != nullptr ){
485 // std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
488 // std::cout << " has no donor[0] and" ;
490 // if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
491 // std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
494 // std::cout << " has no acceptor[0]" ;
496 // std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
497 // if ( (*ResInfoMap)[i].donor[1] != nullptr ){
498 // std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
501 // std::cout << " has no donor[1] and" ;
503 // if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
504 // std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
507 // std::cout << " has no acceptor[1]" ;
513 for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
514 for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
515 if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
516 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
523 if(SecondaryStructuresStatusMap.size() > 1){
524 for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
525 if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
526 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
527 SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
533 return SecondaryStructuresStringLine;
536 secondaryStructures::~secondaryStructures(){
537 SecondaryStructuresStatusMap.resize(0);
538 SecondaryStructuresStringLine.resize(0);
541 DsspTool::DsspStorage::DsspStorage(){
542 storaged_data.resize(0);
545 void DsspTool::DsspStorage::clearAll(){
546 storaged_data.resize(0);
549 std::mutex DsspTool::DsspStorage::mx;
551 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
552 std::lock_guard<std::mutex> guardian(mx);
553 std::pair<int, std::string> datapair(frnr, data);
554 storaged_data.push_back(datapair);
557 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
558 std::sort(storaged_data.begin(), storaged_data.end());
559 return storaged_data;
562 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
563 cutoff = cutoff_init;
566 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
567 while (coordinate < 0) {
568 coordinate += vector_length;
570 while (coordinate >= vector_length) {
571 coordinate -= vector_length;
575 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
584 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
585 rvec coordinates, box_vector_length;
586 num_of_miniboxes.resize(0);
587 num_of_miniboxes.resize(3);
588 for (std::size_t i{XX}; i <= ZZ; ++i) {
589 box_vector_length[i] = std::sqrt(
590 std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
591 num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
593 MiniBoxesMap.resize(0);
594 MiniBoxesReverseMap.resize(0);
595 MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
596 num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
597 num_of_miniboxes[ZZ], std::vector<std::size_t>(
599 MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
600 for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
601 for (std::size_t j{XX}; j <= ZZ; ++j) {
602 coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
603 FixAtomCoordinates(coordinates[j], box_vector_length[j]);
605 MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
606 coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
607 for (std::size_t j{XX}; j <= ZZ; ++j){
608 MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
613 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
614 GetMiniBoxesMap(fr, IndexMap);
615 MiniBoxSize[XX] = MiniBoxesMap.size();
616 MiniBoxSize[YY] = MiniBoxesMap.front().size();
617 MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
619 PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
620 ResiI = PairMap.begin();
621 ResiJ = ResiI->begin();
623 for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
624 for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
625 for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
626 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
627 for (std::size_t k{XX}; k <= ZZ; ++k) {
628 fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
629 ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
631 for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
632 if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
633 PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
634 PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
643 bool alternateNeighborhoodSearch::findNextPair(){
649 for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
650 for(; ResiJ != ResiI->end(); ++ResiJ){
652 resiIpos = ResiI - PairMap.begin();
653 resiJpos = ResiJ - ResiI->begin();
654 if ( ResiJ != ResiI->end() ){
657 else if (ResiI != PairMap.end()) {
659 ResiJ = ResiI->begin();
672 std::size_t alternateNeighborhoodSearch::getResiI() const {
676 std::size_t alternateNeighborhoodSearch::getResiJ() const {
681 DsspTool::DsspStorage DsspTool::Storage;
683 DsspTool::DsspTool(){
686 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
688 const float benddegree{ 70.0 }, maxdist{ 2.5 };
689 float degree{ 0 }, vdist{ 0 }, vprod{ 0 };
690 gmx::RVec a{ 0, 0, 0 }, b{ 0, 0, 0 };
691 for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
693 if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
694 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
699 PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
700 PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
702 // std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
705 for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
707 if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
708 PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
709 PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
710 PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
715 for (int j{ 0 }; j < 3; ++j)
717 a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
718 - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
719 b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
720 - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
722 vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
723 vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
724 IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
727 * gmx::c_angstrom / gmx::c_nano
728 * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
729 IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
732 * gmx::c_angstrom / gmx::c_nano;
733 degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
734 if (degree > benddegree)
736 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
741 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
743 const t_trxframe& fr,
747 * DSSP uses eq from dssp 2.x
748 * kCouplingConstant = 27.888, // = 332 * 0.42 * 0.2
749 * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
753 * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
757 if (CalculateAtomicDistances(
758 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
759 >= minimalCAdistance)
764 const float kCouplingConstant = 27.888;
765 const float minimalAtomDistance{ 0.5 },
767 float HbondEnergy{ 0 };
768 float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
770 // std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
772 if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
773 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
774 distanceNO = CalculateAtomicDistances(
775 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
776 distanceNC = CalculateAtomicDistances(
777 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
778 if (initParams.addHydrogens){
779 if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
781 float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
782 for (int i{XX}; i <= ZZ; ++i){
783 float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
784 atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
785 atomH[i] += prevCO / prevCODist;
787 distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
788 distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
791 distanceHO = distanceNO;
792 distanceHC = distanceNC;
796 distanceHO = CalculateAtomicDistances(
797 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
798 distanceHC = CalculateAtomicDistances(
799 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
801 if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
802 || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
804 HbondEnergy = minEnergy;
809 * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
812 // std::cout << "CA-CA distance: " << CalculateAtomicDistances(
813 // Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
814 // std::cout << "N-O distance: " << distanceNO << std::endl;
815 // std::cout << "N-C distance: " << distanceNC << std::endl;
816 // std::cout << "H-O distance: " << distanceHO << std::endl;
817 // std::cout << "H-C distance: " << distanceHC << std::endl;
819 HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
821 // if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
822 // HbondEnergy = minEnergy;
825 // std::cout << "Calculated energy = " << HbondEnergy << std::endl;
828 // std::cout << "Donor Is Proline" << std::endl;
831 if (HbondEnergy < Donor.acceptorEnergy[0]){
832 Donor.acceptor[1] = Donor.acceptor[0];
833 Donor.acceptor[0] = Acceptor.info;
834 Donor.acceptorEnergy[0] = HbondEnergy;
836 else if (HbondEnergy < Donor.acceptorEnergy[1]){
837 Donor.acceptor[1] = Acceptor.info;
838 Donor.acceptorEnergy[1] = HbondEnergy;
841 if (HbondEnergy < Acceptor.donorEnergy[0]){
842 Acceptor.donor[1] = Acceptor.donor[0];
843 Acceptor.donor[0] = Donor.info;
844 Acceptor.donorEnergy[0] = HbondEnergy;
846 else if (HbondEnergy < Acceptor.donorEnergy[1]){
847 Acceptor.donor[1] = Donor.info;
848 Acceptor.donorEnergy[1] = HbondEnergy;
853 /* Calculate Distance From B to A */
854 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
856 gmx::RVec r{ 0, 0, 0 };
857 pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
858 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
861 /* Calculate Distance From B to A, where A is only fake coordinates */
862 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
864 gmx::RVec r{ 0, 0, 0 };
865 pbc_dx(pbc, A, fr.x[B], r.as_vec());
866 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
869 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
871 initParams = initParamz;
872 ResInfo _backboneAtoms;
875 int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
877 IndexMap.push_back(_backboneAtoms);
878 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
879 proLINE = *(IndexMap[i].info->name);
880 if( proLINE.compare("PRO") == 0 ){
881 IndexMap[i].is_proline = true;
884 for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
885 if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
888 resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
889 IndexMap.emplace_back(_backboneAtoms);
890 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
891 proLINE = *(IndexMap[i].info->name);
892 if( proLINE.compare("PRO") == 0 ){
893 IndexMap[i].is_proline = true;
897 std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
898 if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
900 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
902 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
904 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
906 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
908 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
910 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
912 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
913 if (initParamz.addHydrogens == true){
914 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
917 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
919 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
924 // if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
925 // || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
926 // std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
930 for (std::size_t j {1}; j < IndexMap.size(); ++j){
931 IndexMap[j].prevResi = &(IndexMap[j - 1]);
933 IndexMap[j - 1].nextResi = &(IndexMap[j]);
935 // std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
936 // std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
937 // std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
938 // std::cout << IndexMap[j].prevResi->info->nr;
939 // std::cout << *(IndexMap[j].prevResi->info->name) ;
940 // std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
941 // std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
942 // std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
943 // std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
944 // std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
950 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
953 switch(initParams.NBS){
954 case (NBSearchMethod::Classique): {
956 // store positions of CA atoms to use them for nbSearch
957 std::vector<gmx::RVec> positionsCA_;
958 for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
960 positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
963 AnalysisNeighborhood nb_;
964 nb_.setCutoff(initParams.cutoff_);
965 AnalysisNeighborhoodPositions nbPos_(positionsCA_);
966 gmx::AnalysisNeighborhoodSearch start = nb_.initSearch(pbc, nbPos_);
967 gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
968 gmx::AnalysisNeighborhoodPair pair;
969 while (pairSearch.findNextPair(&pair))
971 if(CalculateAtomicDistances(
972 IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
973 < minimalCAdistance){
974 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
975 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
976 calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
983 case (NBSearchMethod::Experimental): { // TODO FIX
985 alternateNeighborhoodSearch as_;
987 as_.setCutoff(initParams.cutoff_);
989 as_.AltPairSearch(fr, IndexMap);
991 while (as_.findNextPair()){
992 if(CalculateAtomicDistances(
993 IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
994 < minimalCAdistance){
995 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
996 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
997 calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
1006 for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
1007 for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
1008 if(CalculateAtomicDistances(
1009 Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1010 < minimalCAdistance){
1011 calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
1012 if (Acceptor != Donor + 1){
1013 calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
1023 // for(std::size_t i {0}; i < IndexMap.size(); ++i){
1024 // std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
1027 PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
1028 calculateBends(fr, pbc);
1029 Storage.storageData(frnr, PatternSearch.patternSearch());
1033 std::vector<std::pair<int, std::string>> DsspTool::getData(){
1034 return Storage.returnData();
1037 } // namespace analysismodules