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37 * Implements gmx::analysismodules::Trajectory.
39 * \author Sergey Gorelov <Infinity2573@gmail.com>
40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
41 * \author Alexey Shvetsov <alexxyum@gmail.com>
42 * \ingroup module_trajectoryanalysis
45 #include "dssptools.h"
48 #include "gromacs/math/units.h"
50 #include "gromacs/pbcutil/pbc.h"
51 #include <gromacs/trajectoryanalysis.h>
52 #include "gromacs/trajectoryanalysis/topologyinformation.h"
61 namespace analysismodules
64 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
66 // _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
69 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
71 // return _ResInfo[static_cast<std::size_t>(atomTypeName)];
74 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
75 return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
78 secondaryStructures::secondaryStructures(){
80 void secondaryStructures::initiateSearch(const std::vector<ResInfo> &ResInfoMatrix, const bool PiHelicesPreferencez, const int _pp_stretch){
81 SecondaryStructuresStatusMap.resize(0);
82 SecondaryStructuresStringLine.resize(0);
83 std::vector<std::size_t> temp; temp.resize(0),
84 PiHelixPreference = PiHelicesPreferencez;
85 ResInfoMap = &ResInfoMatrix;
86 SecondaryStructuresStatusMap.resize(ResInfoMatrix.size());
87 SecondaryStructuresStringLine.resize(ResInfoMatrix.size(), '~');
90 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName, bool status){
91 SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = status;
93 SecondaryStructuresStatus = secondaryStructureTypeName;
96 SecondaryStructuresStatus = secondaryStructureTypes::Loop;
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 ){
188 // else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
189 // (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
190 // (*ResInfoMap)[Donor].info == nullptr )) {
191 // std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
192 // 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;
193 // std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
194 // 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;
195 // std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
196 // if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
197 // ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
198 // std::cout << "HBond Exist" << std::endl;
202 // std::cout << "Bad hbond check. Reason(s): " ;
203 // if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
204 // std::cout << "Acceptor has no donor[0]; ";
206 // if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
207 // std::cout << "Acceptor has no donor[1]; ";
209 // if ( (*ResInfoMap)[Donor].info == nullptr ){
210 // std::cout << "No info about donor; ";
212 // std::cout << std::endl;
215 return (( ((*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info) && ((*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff )) ||
216 ( ((*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info) && ((*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff )) );
221 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
222 std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
228 if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
229 // std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
236 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
237 if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){ // Protection from idiotz, не обязательно нужен
238 return bridgeTypes::None;
241 ResInfo a{(*ResInfoMap)[i]}, b{(*ResInfoMap)[j]};
243 if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1) && a.prevResi && a.nextResi && b.prevResi && b.nextResi){
244 if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){
245 return bridgeTypes::ParallelBridge;
247 else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){
248 return bridgeTypes::AntiParallelBridge;
251 return bridgeTypes::None;
254 void secondaryStructures::analyzeBridgesAndStrandsPatterns(){
256 for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
257 for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
258 switch(calculateBridge(i, j)){
259 case bridgeTypes::ParallelBridge : {
260 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::ParallelBridge);
261 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
262 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::ParallelBridge);
263 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
266 case bridgeTypes::AntiParallelBridge : {
267 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::AntiParallelBridge);
268 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
269 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::AntiParallelBridge);
270 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
278 // Calculate Extended Strandz
279 for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
280 bool is_Estrand {false};
281 for(std::size_t j {2}; j != 0; --j){
282 for(const bridgeTypes &bridgeType : {bridgeTypes::ParallelBridge, bridgeTypes::AntiParallelBridge}){
283 if (SecondaryStructuresStatusMap[i].hasBridges(bridgeType) && SecondaryStructuresStatusMap[i + j].hasBridges(bridgeType) ){
284 std::size_t i_partner{SecondaryStructuresStatusMap[i].getBridgePartnerIndex(bridgeType)}, j_partner{SecondaryStructuresStatusMap[i + j].getBridgePartnerIndex(bridgeType)}, second_strand{};
285 if ( abs(i_partner - j_partner) < 6){
286 if (i_partner < j_partner){
287 second_strand = i_partner;
290 second_strand = j_partner;
292 for(int k{abs(i_partner - j_partner)}; k >= 0; --k){
293 if (SecondaryStructuresStatusMap[second_strand + k].getStatus(secondaryStructureTypes::Bridge)){
294 SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Bridge, false);
297 SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Strand);
304 for(std::size_t k{0}; k <= j; ++k){
305 if (SecondaryStructuresStatusMap[i + k].getStatus(secondaryStructureTypes::Bridge)){
306 SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Bridge, false);
308 SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Strand);
326 // for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
327 // for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
328 // if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
329 // if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1]) ||
330 // (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
331 // Bridge[i].push_back(j);
333 // if ((HBondsMap[i][j] && HBondsMap[j][i]) ||
334 // (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
335 // AntiBridge[i].push_back(j);
340 // for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
341 // if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
342 // setStatus(i, secondaryStructureTypes::Bulge);
345 // for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
346 // for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
351 // for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
352 // if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
353 // for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
354 // for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
355 // if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
356 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
357 // && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
358 // - static_cast<int>(getBridge(*bridge)[j][j_resi]))
361 // for (std::size_t k{ 0 }; k <= i - j; ++k){
362 // setStatus(i + k, secondaryStructureTypes::Ladder);
366 // for (std::size_t k{ 0 }; k <= j - i; ++k){
367 // setStatus(i + k, secondaryStructureTypes::Ladder);
380 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
381 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
382 std::size_t stride {static_cast<std::size_t>(i) + 3};
383 for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
384 if (hasHBondBetween(j + stride, j)){
385 std::cout << "Bond between " << j << " and " << j + stride << " exists" << std::endl;
387 if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
388 // std::cout << "Resi " << j << " is Helix_" << stride << " start" << std::endl;
389 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
391 for (std::size_t k {1}; k < stride; ++k){
392 if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
393 SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
394 // SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
398 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
399 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
402 SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
408 for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
409 std::size_t stride {static_cast<std::size_t>(i) + 3};
410 for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
411 if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
412 (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
414 secondaryStructureTypes Helix;
416 case turnsTypes::Turn_3:
417 for (std::size_t k {0}; empty && k < stride; ++k){
418 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
420 Helix = secondaryStructureTypes::Helix_3;
422 case turnsTypes::Turn_5:
423 for (std::size_t k {0}; empty && k < stride; ++k){
424 empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
426 Helix = secondaryStructureTypes::Helix_5;
429 Helix = secondaryStructureTypes::Helix_4;
432 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
433 for(std::size_t k {0}; k < stride; ++k ){
434 // std::cout << "Resi " << j << " is Helix_" << static_cast<std::size_t>(Helix) - 5 << std::endl;
435 SecondaryStructuresStatusMap[j + k].setStatus(Helix);
442 /* Не знаю зач они в дссп так сделали, этож полное говно */
444 for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
445 if (static_cast<int>(SecondaryStructuresStatusMap[i].getStatus()) <= static_cast<int>(secondaryStructureTypes::Turn)){
447 for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
448 std::size_t stride {static_cast<std::size_t>(j) + 3};
449 for(std::size_t k {1}; k < stride and !isTurn; ++k){
450 isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
454 // std::cout << "Resi " << i << " is Turn" << std::endl;
455 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
462 std::string secondaryStructures::patternSearch(){
465 analyzeBridgesAndStrandsPatterns();
466 analyzeTurnsAndHelicesPatterns();
468 // for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
469 // std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
472 std::cout.precision(5);
473 for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
474 std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
475 if ( (*ResInfoMap)[i].donor[0] != nullptr ){
476 std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
479 std::cout << " has no donor[0] and" ;
481 if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
482 std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
485 std::cout << " has no acceptor[0]" ;
487 std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
488 if ( (*ResInfoMap)[i].donor[1] != nullptr ){
489 std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
492 std::cout << " has no donor[1] and" ;
494 if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
495 std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
498 std::cout << " has no acceptor[1]" ;
504 for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
505 for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
506 if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
507 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
514 if(SecondaryStructuresStatusMap.size() > 1){
515 for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
516 if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
517 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
518 SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
524 return SecondaryStructuresStringLine;
527 secondaryStructures::~secondaryStructures(){
528 SecondaryStructuresStatusMap.resize(0);
529 SecondaryStructuresStringLine.resize(0);
532 DsspTool::DsspStorage::DsspStorage(){
533 storaged_data.resize(0);
536 void DsspTool::DsspStorage::clearAll(){
537 storaged_data.resize(0);
540 std::mutex DsspTool::DsspStorage::mx;
542 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
543 std::lock_guard<std::mutex> guardian(mx);
544 std::pair<int, std::string> datapair(frnr, data);
545 storaged_data.push_back(datapair);
548 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
549 std::sort(storaged_data.begin(), storaged_data.end());
550 return storaged_data;
553 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
554 cutoff = cutoff_init;
557 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
558 while (coordinate < 0) {
559 coordinate += vector_length;
561 while (coordinate >= vector_length) {
562 coordinate -= vector_length;
566 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
575 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
576 rvec coordinates, box_vector_length;
577 num_of_miniboxes.resize(0);
578 num_of_miniboxes.resize(3);
579 for (std::size_t i{XX}; i <= ZZ; ++i) {
580 box_vector_length[i] = std::sqrt(
581 std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
582 num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
584 MiniBoxesMap.resize(0);
585 MiniBoxesReverseMap.resize(0);
586 MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
587 num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
588 num_of_miniboxes[ZZ], std::vector<std::size_t>(
590 MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
591 for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
592 for (std::size_t j{XX}; j <= ZZ; ++j) {
593 coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
594 FixAtomCoordinates(coordinates[j], box_vector_length[j]);
596 MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
597 coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
598 for (std::size_t j{XX}; j <= ZZ; ++j){
599 MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
604 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
605 GetMiniBoxesMap(fr, IndexMap);
606 MiniBoxSize[XX] = MiniBoxesMap.size();
607 MiniBoxSize[YY] = MiniBoxesMap.front().size();
608 MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
610 PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
611 ResiI = PairMap.begin();
612 ResiJ = ResiI->begin();
614 for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
615 for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
616 for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
617 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
618 for (std::size_t k{XX}; k <= ZZ; ++k) {
619 fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
620 ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
622 for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
623 if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
624 PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
625 PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
634 bool alternateNeighborhoodSearch::findNextPair(){
640 for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
641 for(; ResiJ != ResiI->end(); ++ResiJ){
643 resiIpos = ResiI - PairMap.begin();
644 resiJpos = ResiJ - ResiI->begin();
645 if ( ResiJ != ResiI->end() ){
648 else if (ResiI != PairMap.end()) {
650 ResiJ = ResiI->begin();
663 std::size_t alternateNeighborhoodSearch::getResiI() const {
667 std::size_t alternateNeighborhoodSearch::getResiJ() const {
672 DsspTool::DsspStorage DsspTool::Storage;
674 DsspTool::DsspTool(){
677 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
679 const float benddegree{ 70.0 }, maxdist{ 2.5 };
680 float degree{ 0 }, vdist{ 0 }, vprod{ 0 };
681 gmx::RVec a{ 0, 0, 0 }, b{ 0, 0, 0 };
682 for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
684 if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
685 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
690 PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
691 PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
693 // std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
696 for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
698 if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
699 PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
700 PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
701 PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
706 for (int j{ 0 }; j < 3; ++j)
708 a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
709 - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
710 b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
711 - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
713 vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
714 vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
715 IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
718 * gmx::c_angstrom / gmx::c_nano
719 * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
720 IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
723 * gmx::c_angstrom / gmx::c_nano;
724 degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
725 if (degree > benddegree)
727 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
732 float DsspTool::CalculateDihedralAngle(const int &A, const int &B, const int &C, const int &D, const t_trxframe &fr, const t_pbc *pbc){
733 float result{360}, u{}, v{};
734 gmx::RVec v12{}, v43{}, z{}, p{}, x{}, y{};
735 pbc_dx(pbc, fr.x[A], fr.x[B], v12.as_vec());
736 pbc_dx(pbc, fr.x[D], fr.x[C], v43.as_vec());
737 pbc_dx(pbc, fr.x[B], fr.x[C], z.as_vec());
739 for(std::size_t j {XX}; j <= ZZ; ++j){
740 v12[j] *= gmx::c_nm2A;
741 v43[j] *= gmx::c_nm2A;
744 for(std::size_t i{XX}, j{i + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
751 p[i] = (z[j] * v12[k]) - (z[k] * v12[j]);
752 x[i] = (z[j] * v43[k]) - (z[k] * v43[j]);
755 for(std::size_t i{XX}, j{i + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
762 y[i] = (z[j] * x[k]) - (z[k] * x[j]);
765 // std::cout << "v12 = " << v12[0] << ", " << v12[1] << ", " << v12[2] << std::endl;
766 // std::cout << "v43 = " << v43[0] << ", " << v43[1] << ", " << v43[2] << std::endl;
767 // std::cout << "z = " << z[0] << ", " << z[1] << ", " << z[2] << std::endl;
768 // std::cout << "p = " << p[0] << ", " << p[1] << ", " << p[2] << std::endl;
769 // std::cout << "x = " << x[0] << ", " << x[1] << ", " << x[2] << std::endl;
770 // std::cout << "y = " << y[0] << ", " << y[1] << ", " << y[2] << std::endl;
772 u = (x[XX] * x[XX]) + (x[YY] * x[YY]) + (x[ZZ] * x[ZZ]);
773 v = (y[XX] * y[XX]) + (y[YY] * y[YY]) + (y[ZZ] * y[ZZ]);
775 // std::cout << "u = " << u << std::endl;
776 // std::cout << "v = " << v << std::endl;
778 if (u > 0 and v > 0){
779 u = ((p[XX] * x[XX]) + (p[YY] * x[YY]) + (p[ZZ] * x[ZZ])) / std::sqrt(u);
780 v = ((p[XX] * y[XX]) + (p[YY] * y[YY]) + (p[ZZ] * y[ZZ])) / std::sqrt(v);
781 // std::cout << "new u = " << u << std::endl;
782 // std::cout << "new v = " << v << std::endl;
783 if (u != 0 or v != 0){
784 result = std::atan2(v, u) * gmx::c_rad2Deg;
785 // std::cout << "result = " << result << std::endl;
791 void DsspTool::calculateDihedrals(const t_trxframe &fr, const t_pbc *pbc){
792 const float epsilon = 29;
793 const float phi_min = -75 - epsilon; // -104
794 const float phi_max = -75 + epsilon; // -46
795 const float psi_min = 145 - epsilon; // 116
796 const float psi_max = 145 + epsilon; // 176
797 std::vector<float> phi(IndexMap.size(), 360), psi(IndexMap.size(), 360);
800 // phi.resize(IndexMap.size(), 360);
801 // psi.resize(IndexMap.size(), 360);
803 for (std::size_t i = 1; i + 1 < IndexMap.size(); ++i){ // TODO add index verifictaion (check if those atom indexes exist)
804 // std::cout << "For resi " << i << " :" << std::endl;
805 phi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i - 1].getIndex(backboneAtomTypes::AtomC)),
806 static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
807 static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
808 static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
811 psi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
812 static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
813 static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
814 static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
817 // std::cout << "For " << i << " phi = " << phi[i] << ", psi = " << psi[i] << std::endl;
818 // std::cout << "phi[" << i << "] = " << phi[i] << std::endl;
819 // std::cout << "psi[" << i << "] = " << psi[i] << std::endl;
822 for (std::size_t i = 1; i + 3 < IndexMap.size(); ++i){
823 switch (initParams.pp_stretch){
825 if (phi_min > phi[i] or phi[i] > phi_max or
826 phi_min > phi[i + 1] or phi[i + 1]> phi_max){
830 if (psi_min > psi[i] or psi[i] > psi_max or
831 psi_min > psi[i + 1] or psi[i + 1] > psi_max){
835 switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
836 case HelixPositions::None:
837 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
840 case HelixPositions::End:
841 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
848 PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
849 /* Пропустил проверку того, что заменяемая ак - петля */
850 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
851 PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
855 if (phi_min > phi[i] or phi[i] > phi_max or
856 phi_min > phi[i + 1] or phi[i + 1]> phi_max or
857 phi_min > phi[i + 2] or phi[i + 2]> phi_max){
861 if (psi_min > psi[i] or psi[i] > psi_max or
862 psi_min > psi[i + 1] or psi[i + 1] > psi_max or
863 psi_min > psi[i + 2] or psi[i + 2] > psi_max){
867 switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
868 case HelixPositions::None:
869 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
872 case HelixPositions::End:
873 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
880 PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::Middle, turnsTypes::Turn_PP);
881 PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
882 /* Пропустил проверку того, что заменяемая ак - петля */
883 PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
884 PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
885 PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(secondaryStructureTypes::Helix_PP);
890 throw std::runtime_error("Unsupported stretch length");
896 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
898 const t_trxframe& fr,
902 * DSSP uses eq from dssp 2.x
903 * kCouplingConstant = 27.888, // = 332 * 0.42 * 0.2
904 * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
908 * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
912 if (CalculateAtomicDistances(
913 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
914 >= minimalCAdistance)
919 const float kCouplingConstant = 27.888;
920 const float minimalAtomDistance{ 0.5 },
922 float HbondEnergy{ 0 };
923 float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
925 // std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
927 if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
928 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
929 distanceNO = CalculateAtomicDistances(
930 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
931 distanceNC = CalculateAtomicDistances(
932 Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
933 if (initParams.addHydrogens){
934 if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
936 float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
937 for (int i{XX}; i <= ZZ; ++i){
938 float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
939 atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
940 atomH[i] += prevCO / prevCODist;
942 distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
943 distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
946 distanceHO = distanceNO;
947 distanceHC = distanceNC;
951 distanceHO = CalculateAtomicDistances(
952 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
953 distanceHC = CalculateAtomicDistances(
954 Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
956 if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
957 || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
959 HbondEnergy = minEnergy;
964 * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
967 // std::cout << "CA-CA distance: " << CalculateAtomicDistances(
968 // Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
969 // std::cout << "N-O distance: " << distanceNO << std::endl;
970 // std::cout << "N-C distance: " << distanceNC << std::endl;
971 // std::cout << "H-O distance: " << distanceHO << std::endl;
972 // std::cout << "H-C distance: " << distanceHC << std::endl;
974 HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
976 if ( HbondEnergy < minEnergy ){
977 HbondEnergy = minEnergy;
980 // std::cout << "Calculated energy = " << HbondEnergy << std::endl;
983 // std::cout << "Donor Is Proline" << std::endl;
986 if (HbondEnergy < Donor.acceptorEnergy[0]){
987 Donor.acceptor[1] = Donor.acceptor[0];
988 Donor.acceptor[0] = Acceptor.info;
989 Donor.acceptorEnergy[0] = HbondEnergy;
991 else if (HbondEnergy < Donor.acceptorEnergy[1]){
992 Donor.acceptor[1] = Acceptor.info;
993 Donor.acceptorEnergy[1] = HbondEnergy;
996 if (HbondEnergy < Acceptor.donorEnergy[0]){
997 Acceptor.donor[1] = Acceptor.donor[0];
998 Acceptor.donor[0] = Donor.info;
999 Acceptor.donorEnergy[0] = HbondEnergy;
1001 else if (HbondEnergy < Acceptor.donorEnergy[1]){
1002 Acceptor.donor[1] = Donor.info;
1003 Acceptor.donorEnergy[1] = HbondEnergy;
1008 /* Calculate Distance From B to A */
1009 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1011 gmx::RVec r{ 0, 0, 0 };
1012 pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
1013 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1016 /* Calculate Distance From B to A, where A is only fake coordinates */
1017 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1019 gmx::RVec r{ 0, 0, 0 };
1020 pbc_dx(pbc, A, fr.x[B], r.as_vec());
1021 return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1024 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
1026 initParams = initParamz;
1027 ResInfo _backboneAtoms;
1029 std::string proLINE;
1030 int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
1032 IndexMap.push_back(_backboneAtoms);
1033 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1034 proLINE = *(IndexMap[i].info->name);
1035 if( proLINE.compare("PRO") == 0 ){
1036 IndexMap[i].is_proline = true;
1039 for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
1040 if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
1043 resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
1044 IndexMap.emplace_back(_backboneAtoms);
1045 IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1046 proLINE = *(IndexMap[i].info->name);
1047 if( proLINE.compare("PRO") == 0 ){
1048 IndexMap[i].is_proline = true;
1052 std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
1053 if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
1055 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
1057 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
1059 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
1061 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
1063 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
1065 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
1067 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
1068 if (initParamz.addHydrogens == true){
1069 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1072 else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
1074 IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1079 // if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
1080 // || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
1081 // std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
1085 for (std::size_t j {1}; j < IndexMap.size(); ++j){
1086 IndexMap[j].prevResi = &(IndexMap[j - 1]);
1088 IndexMap[j - 1].nextResi = &(IndexMap[j]);
1090 // std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
1091 // std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
1092 // std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
1093 // std::cout << IndexMap[j].prevResi->info->nr;
1094 // std::cout << *(IndexMap[j].prevResi->info->name) ;
1095 // std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
1096 // std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
1097 // std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
1098 // std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
1099 // std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
1105 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
1108 switch(initParams.NBS){
1109 case (NBSearchMethod::Classique): {
1111 // store positions of CA atoms to use them for nbSearch
1112 std::vector<gmx::RVec> positionsCA_;
1113 for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
1115 positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
1118 AnalysisNeighborhood nb_;
1119 nb_.setCutoff(initParams.cutoff_);
1120 AnalysisNeighborhoodPositions nbPos_(positionsCA_);
1121 gmx::AnalysisNeighborhoodSearch start = nb_.initSearch(pbc, nbPos_);
1122 gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
1123 gmx::AnalysisNeighborhoodPair pair;
1124 while (pairSearch.findNextPair(&pair))
1126 if(CalculateAtomicDistances(
1127 IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1128 < minimalCAdistance){
1129 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
1130 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
1131 calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
1138 case (NBSearchMethod::Experimental): { // TODO FIX
1140 alternateNeighborhoodSearch as_;
1142 as_.setCutoff(initParams.cutoff_);
1144 as_.AltPairSearch(fr, IndexMap);
1146 while (as_.findNextPair()){
1147 if(CalculateAtomicDistances(
1148 IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1149 < minimalCAdistance){
1150 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
1151 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
1152 calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
1161 for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
1162 for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
1163 if(CalculateAtomicDistances(
1164 Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1165 < minimalCAdistance){
1166 calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
1167 if (Acceptor != Donor + 1){
1168 calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
1178 // for(std::size_t i {0}; i < IndexMap.size(); ++i){
1179 // std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
1182 PatternSearch.initiateSearch(IndexMap, initParams.PPHelices, initParams.pp_stretch);
1183 calculateBends(fr, pbc);
1184 calculateDihedrals(fr, pbc);
1185 Storage.storageData(frnr, PatternSearch.patternSearch());
1189 std::vector<std::pair<int, std::string>> DsspTool::getData(){
1190 return Storage.returnData();
1193 } // namespace analysismodules