src/dssptools.cpp

   1 /*
   2 * This file is part of the GROMACS molecular simulation package.
   3 *
   4 * Copyright (c) 2021, by the GROMACS development team, led by
   5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 * and including many others, as listed in the AUTHORS file in the
   7 * top-level source directory and at http://www.gromacs.org.
   8 *
   9 * GROMACS is free software; you can redistribute it and/or
  10 * modify it under the terms of the GNU Lesser General Public License
  11 * as published by the Free Software Foundation; either version 2.1
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  13 *
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  17 * Lesser General Public License for more details.
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  35 /*! \internal \file
  36 * \brief
  37 * Implements gmx::analysismodules::Trajectory.
  38 *
  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
  43 */
  44
  45 /*
  46     There's something wrong with energy calculations of redidues with E ≈ -0
  47 */
  48
  49
  50 #include "dssptools.h"
  51
  52 #include <algorithm>
  53 #include "gromacs/math/units.h"
  54
  55 #include "gromacs/pbcutil/pbc.h"
  56 #include <gromacs/trajectoryanalysis.h>
  57 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  58 #include <set>
  59 #include <fstream>
  60 #include <mutex>
  61 #include <iostream>
  62
  63 namespace gmx
  64 {
  65
  66 namespace analysismodules
  67 {
  68
  69 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
  70 //{
  71 //   _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
  72 //}
  73
  74 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
  75 //{
  76 //   return _ResInfo[static_cast<std::size_t>(atomTypeName)];
  77 //}
  78
  79 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
  80     return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
  81 }
  82
  83 secondaryStructures::secondaryStructures(){
  84 }
  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(), '~');
  93 }
  94
  95 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName){
  96     SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = true;
  97     SecondaryStructuresStatus = secondaryStructureTypeName;
  98 }
  99
 100 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
 101     TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
 102 }
 103
 104 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
 105     return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
 106 }
 107
 108 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
 109     return breakPartners[0] == partner || breakPartners[1] == partner;
 110 }
 111
 112 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
 113     return TurnsStatusArray[static_cast<std::size_t>(turn)];
 114 }
 115
 116 secondaryStructureTypes secondaryStructures::secondaryStructuresData::getStatus() const{
 117     return  SecondaryStructuresStatus;
 118 }
 119
 120 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
 121     if (breakPartners[0] == nullptr){
 122         breakPartners[0] = breakPartner;
 123     }
 124     else{
 125         breakPartners[1] = breakPartner;
 126     }
 127     setStatus(secondaryStructureTypes::Break);
 128 }
 129
 130 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
 131     if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
 132         (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
 133         (*ResInfoMap)[Acceptor].info == nullptr ){
 134         std::cout << "Bad hbond check. Reason(s): " ;
 135         if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 136             std::cout << "Donor has no acceptor[0]; ";
 137         }
 138         if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 139             std::cout << "Donor has no acceptor[1]; ";
 140         }
 141         if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 142             std::cout << "No info about acceptor; ";
 143         }
 144         std::cout << std::endl;
 145         return false;
 146     }
 147 //    else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
 148 //              (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
 149 //              (*ResInfoMap)[Donor].info == nullptr )) {
 150 //        std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
 151 //        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;
 152 //        std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
 153 //        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;
 154 //        std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
 155 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 156 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 157 //            std::cout << "HBond Exist" << std::endl;
 158 //        }
 159 //    }
 160 //    else {
 161 //        std::cout << "Bad hbond check. Reason(s): " ;
 162 //        if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
 163 //            std::cout << "Acceptor has no donor[0]; ";
 164 //        }
 165 //        if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
 166 //            std::cout << "Acceptor has no donor[1]; ";
 167 //        }
 168 //        if ( (*ResInfoMap)[Donor].info == nullptr ){
 169 //            std::cout << "No info about donor; ";
 170 //        }
 171 //        std::cout << std::endl;
 172 //    }
 173
 174     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 175            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 176
 177
 178 }
 179
 180 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 181     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 182     if ( i > j ){
 183         std::swap(i, j);
 184     }
 185
 186     for (; i != j; ++i){
 187         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 188             std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 189             return false;
 190         }
 191     }
 192     return true;
 193 }
 194
 195 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 196     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
 197         return bridgeTypes::None;
 198     }
 199     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
 200         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
 201             return bridgeTypes::ParallelBridge;
 202         }
 203         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
 204             return bridgeTypes::AntiParallelBridge;
 205         }
 206     }
 207     return bridgeTypes::None;
 208 }
 209
 210 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 211     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 212         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 213             bridgeTypes type {calculateBridge(i, j)};
 214             if (type == bridgeTypes::None){
 215                 continue;
 216             }
 217             bool found {false};
 218         }
 219     }
 220
 221
 222
 223
 224
 225
 226
 227
 228
 229
 230
 231
 232 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 233 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 234 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 235 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 236 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 237 //                    Bridge[i].push_back(j);
 238 //                }
 239 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 240 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 241 //                    AntiBridge[i].push_back(j);
 242 //                }
 243 //            }
 244 //        }
 245 //    }
 246 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 247 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 248 //            setStatus(i, secondaryStructureTypes::Bulge);
 249 //        }
 250 //    }
 251 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 252 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 253 //            if (j == i){
 254 //                continue;
 255 //            }
 256 //            else {
 257 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 258 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 259 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 260 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 261 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 262 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 263 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 264 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 265 //                                        < 5)){
 266 //                                    if (j < i){
 267 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 268 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 269 //                                        }
 270 //                                    }
 271 //                                    else{
 272 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 273 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 274 //                                        }
 275 //                                    }
 276 //                                }
 277 //                            }
 278 //                        }
 279 //                    }
 280 //                }
 281 //            }
 282 //        }
 283 //    }
 284 }
 285
 286 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 287     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 288         std::size_t stride {static_cast<std::size_t>(i) + 3};
 289         std::cout << "Testing Helix_" << stride << std::endl;
 290         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 291             std::cout << "Testing " << j << " and " << j + stride << std::endl;
 292             if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
 293                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 294                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 295
 296                 for (std::size_t k {1}; k < stride; ++k){
 297                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 298                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 299                         SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 300                     }
 301
 302                 }
 303
 304                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 305                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 306                 }
 307                 else {
 308                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 309                 }
 310             }
 311         }
 312     }
 313
 314     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 315         std::size_t stride {static_cast<std::size_t>(i) + 3};
 316         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 317             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 318                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 319                 bool empty = true;
 320                 secondaryStructureTypes Helix;
 321                 switch(i){
 322                 case turnsTypes::Turn_3:
 323                     for (std::size_t k {0}; empty && k < stride; ++k){
 324                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 325                     }
 326                     Helix = secondaryStructureTypes::Helix_3;
 327                     break;
 328                 case turnsTypes::Turn_5:
 329                     for (std::size_t k {0}; empty && k < stride; ++k){
 330                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 331                     }
 332                     Helix = secondaryStructureTypes::Helix_5;
 333                     break;
 334                 default:
 335                     Helix = secondaryStructureTypes::Helix_4;
 336                     break;
 337                 }
 338                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 339                     for(std::size_t k {0}; k < stride; ++k ){
 340                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 341                     }
 342                 }
 343             }
 344         }
 345     }
 346
 347 //    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 348 //        if (SecondaryStructuresStatusMap[i].getStatus() == secondaryStructureTypes::Loop || SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 349 //            bool isTurn = false;
 350 //            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 351 //                std::size_t stride {static_cast<std::size_t>(i) + 3};
 352 //                for(std::size_t k {1}; k < stride; ++k){
 353 //                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 354 //                }
 355 //            }
 356
 357 //            if (isTurn){
 358 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 359 //            }
 360 //        }
 361 //    }
 362
 363 }
 364
 365 void secondaryStructures::analyzePPHelicesPatterns(){}
 366
 367 std::string secondaryStructures::patternSearch(){
 368
 369
 370 //    analyzeBridgesAndLaddersPatterns();
 371     analyzeTurnsAndHelicesPatterns();
 372 //    analyzePPHelicesPatterns();
 373
 374 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 375 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 376 //    }
 377
 378 //    std::cout.precision(5);
 379 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 380 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 381 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 382 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 383 //        }
 384 //        else {
 385 //            std::cout << " has no donor[0] and" ;
 386 //        }
 387 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 388 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 389 //        }
 390 //        else {
 391 //            std::cout << " has no acceptor[0]" ;
 392 //        }
 393 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 394 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 395 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 396 //        }
 397 //        else {
 398 //            std::cout << " has no donor[1] and" ;
 399 //        }
 400 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 401 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 402 //        }
 403 //        else {
 404 //            std::cout << " has no acceptor[1]" ;
 405 //        }
 406 //    }
 407
 408     /*Write Data*/
 409
 410     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 411         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 412             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 413                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 414             }
 415         }
 416     }
 417
 418     /*Add breaks*/
 419
 420     if(SecondaryStructuresStatusMap.size() > 1){
 421         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 422             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 423                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 424                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 425                     ++linefactor;
 426                 }
 427             }
 428         }
 429     }
 430     return SecondaryStructuresStringLine;
 431 }
 432
 433 secondaryStructures::~secondaryStructures(){
 434     SecondaryStructuresStatusMap.resize(0);
 435     SecondaryStructuresStringLine.resize(0);
 436 }
 437
 438 DsspTool::DsspStorage::DsspStorage(){
 439     storaged_data.resize(0);
 440 }
 441
 442 void DsspTool::DsspStorage::clearAll(){
 443     storaged_data.resize(0);
 444 }
 445
 446 std::mutex DsspTool::DsspStorage::mx;
 447
 448 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 449     std::lock_guard<std::mutex> guardian(mx);
 450     std::pair<int, std::string> datapair(frnr, data);
 451     storaged_data.push_back(datapair);
 452 }
 453
 454 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 455     std::sort(storaged_data.begin(), storaged_data.end());
 456     return storaged_data;
 457 }
 458
 459 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 460     cutoff = cutoff_init;
 461 }
 462
 463 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 464     while (coordinate < 0) {
 465         coordinate += vector_length;
 466     }
 467     while (coordinate >= vector_length) {
 468         coordinate -= vector_length;
 469     }
 470 }
 471
 472 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 473     if (x < 0) {
 474         x += x_max;
 475     }
 476     if (x >= x_max) {
 477         x -= x_max;
 478     }
 479 }
 480
 481 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 482     rvec coordinates, box_vector_length;
 483     num_of_miniboxes.resize(0);
 484     num_of_miniboxes.resize(3);
 485     for (std::size_t i{XX}; i <= ZZ; ++i) {
 486         box_vector_length[i] = std::sqrt(
 487                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 488         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 489     }
 490     MiniBoxesMap.resize(0);
 491     MiniBoxesReverseMap.resize(0);
 492     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 493                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 494                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 495                              0))));
 496     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 497     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 498         for (std::size_t j{XX}; j <= ZZ; ++j) {
 499             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 500             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 501         }
 502         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 503                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 504         for (std::size_t j{XX}; j <= ZZ; ++j){
 505             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 506         }
 507     }
 508 }
 509
 510 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 511     GetMiniBoxesMap(fr, IndexMap);
 512     MiniBoxSize[XX] = MiniBoxesMap.size();
 513     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 514     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 515     PairMap.resize(0);
 516     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 517     ResiI = PairMap.begin();
 518     ResiJ = ResiI->begin();
 519
 520     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 521         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 522             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 523                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 524                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 525                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 526                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 527                     }
 528                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 529                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 530                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 531                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 532                         }
 533                     }
 534                 }
 535             }
 536         }
 537     }
 538 }
 539
 540 bool alternateNeighborhoodSearch::findNextPair(){
 541
 542     if(!PairMap.size()){
 543         return false;
 544     }
 545
 546     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 547         for(; ResiJ != ResiI->end(); ++ResiJ){
 548             if(*ResiJ){
 549                 resiIpos = ResiI - PairMap.begin();
 550                 resiJpos = ResiJ - ResiI->begin();
 551                 if ( ResiJ != ResiI->end() ){
 552                     ++ResiJ;
 553                 }
 554                 else if (ResiI != PairMap.end()) {
 555                     ++ResiI;
 556                     ResiJ = ResiI->begin();
 557                 }
 558                 else {
 559                     return false; // ???
 560                 }
 561                 return true;
 562             }
 563         }
 564     }
 565
 566     return false;
 567 }
 568
 569 std::size_t alternateNeighborhoodSearch::getResiI() const {
 570     return resiIpos;
 571 }
 572
 573 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 574     return resiJpos;
 575 }
 576
 577
 578 DsspTool::DsspStorage DsspTool::Storage;
 579
 580 DsspTool::DsspTool(){
 581 }
 582
 583 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 584 {
 585    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 586    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 587    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 588    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 589    {
 590        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 591                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 592                                     fr,
 593                                     pbc)
 594            > maxdist)
 595        {
 596            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 597            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 598
 599 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 600        }
 601    }
 602    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 603    {
 604        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 605            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 606            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 607            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 608           )
 609        {
 610            continue;
 611        }
 612        for (int j{ 0 }; j < 3; ++j)
 613        {
 614            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 615                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 616            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 617                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 618        }
 619        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 620        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 621                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 622                                         fr,
 623                                         pbc)
 624                * gmx::c_angstrom / gmx::c_nano
 625                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 626                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 627                                           fr,
 628                                           pbc)
 629                * gmx::c_angstrom / gmx::c_nano;
 630        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 631        if (degree > benddegree)
 632        {
 633            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 634        }
 635    }
 636 }
 637
 638 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 639                        ResInfo& Acceptor,
 640                        const t_trxframe&          fr,
 641                        const t_pbc*               pbc)
 642 {
 643    /*
 644     * DSSP uses eq from dssp 2.x
 645     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 646     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 647     * if R is in A
 648     * Hbond if E < -0.5
 649     *
 650     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 651     *
 652     */
 653
 654     if (CalculateAtomicDistances(
 655                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 656         >= minimalCAdistance)
 657     {
 658         return void();
 659     }
 660
 661     const float kCouplingConstant = 27.888;
 662     const float minimalAtomDistance{ 0.5 },
 663             minEnergy{ -9.9 };
 664     float HbondEnergy{ 0 };
 665     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 666
 667 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 668
 669     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 670                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 671         distanceNO = CalculateAtomicDistances(
 672                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 673         distanceNC = CalculateAtomicDistances(
 674                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 675         if (initParams.addHydrogens){
 676             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 677                rvec atomH{};
 678                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 679                for (int i{XX}; i <= ZZ; ++i){
 680                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 681                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 682                    atomH[i] += prevCO / prevCODist;
 683                }
 684                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 685                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 686             }
 687             else{
 688                 distanceHO = distanceNO;
 689                 distanceHC = distanceNC;
 690             }
 691        }
 692        else {
 693            distanceHO = CalculateAtomicDistances(
 694                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 695            distanceHC = CalculateAtomicDistances(
 696                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 697        }
 698        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 699         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 700        {
 701             HbondEnergy = minEnergy;
 702        }
 703        else{
 704            HbondEnergy =
 705                    kCouplingConstant
 706                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 707        }
 708
 709 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 710 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 711 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 712 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 713 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 714 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 715
 716        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 717
 718 //       if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
 719 //            HbondEnergy = minEnergy;
 720 //       }
 721
 722 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 723     }
 724 //    else{
 725 //        std::cout << "Donor Is Proline" << std::endl;
 726 //    }
 727
 728     if (HbondEnergy < Donor.acceptorEnergy[0]){
 729            Donor.acceptor[1] = Donor.acceptor[0];
 730            Donor.acceptor[0] = Acceptor.info;
 731            Donor.acceptorEnergy[0] = HbondEnergy;
 732     }
 733     else if (HbondEnergy < Donor.acceptorEnergy[1]){
 734            Donor.acceptor[1] = Acceptor.info;
 735            Donor.acceptorEnergy[1] = HbondEnergy;
 736     }
 737
 738     if (HbondEnergy < Acceptor.donorEnergy[0]){
 739            Acceptor.donor[1] = Acceptor.donor[0];
 740            Acceptor.donor[0] = Donor.info;
 741            Acceptor.donorEnergy[0] = HbondEnergy;
 742     }
 743     else if (HbondEnergy < Acceptor.donorEnergy[1]){
 744            Acceptor.donor[1] = Donor.info;
 745            Acceptor.donorEnergy[1] = HbondEnergy;
 746     }
 747 }
 748
 749
 750 /* Calculate Distance From B to A */
 751 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 752 {
 753    gmx::RVec r{ 0, 0, 0 };
 754    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 755    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 756 }
 757
 758 /* Calculate Distance From B to A, where A is only fake coordinates */
 759 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 760 {
 761    gmx::RVec r{ 0, 0, 0 };
 762    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 763    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 764 }
 765
 766 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 767 {
 768    initParams = initParamz;
 769    ResInfo _backboneAtoms;
 770    std::size_t                 i{ 0 };
 771    std::string proLINE;
 772    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
 773    IndexMap.resize(0);
 774    IndexMap.push_back(_backboneAtoms);
 775    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 776    proLINE = *(IndexMap[i].info->name);
 777    if( proLINE.compare("PRO") == 0 ){
 778        IndexMap[i].is_proline = true;
 779    }
 780
 781    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
 782        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
 783        {
 784            ++i;
 785            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
 786            IndexMap.emplace_back(_backboneAtoms);
 787            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 788            proLINE = *(IndexMap[i].info->name);
 789            if( proLINE.compare("PRO") == 0 ){
 790                IndexMap[i].is_proline = true;
 791            }
 792
 793        }
 794        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
 795        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
 796        {
 797            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
 798        }
 799        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
 800        {
 801            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
 802        }
 803        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
 804        {
 805            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
 806        }
 807        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
 808        {
 809            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
 810            if (initParamz.addHydrogens == true){
 811                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 812            }
 813        }
 814        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 815        {
 816            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 817        }
 818
 819
 820
 821 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 822 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 823 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 824 //       }
 825    }
 826
 827    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 828        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 829
 830        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 831
 832 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 833 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 834 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 835 //         std::cout << IndexMap[j].prevResi->info->nr;
 836 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 837 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 838 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 839 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 840 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 841 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 842    }
 843
 844    nres = i + 1;
 845 }
 846
 847 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 848 {
 849
 850     switch(initParams.NBS){
 851     case (NBSearchMethod::Classique): {
 852
 853         // store positions of CA atoms to use them for nbSearch
 854         std::vector<gmx::RVec> positionsCA_;
 855         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 856         {
 857             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 858         }
 859
 860         AnalysisNeighborhood nb_;
 861         nb_.setCutoff(initParams.cutoff_);
 862         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 863         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 864         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 865         gmx::AnalysisNeighborhoodPair       pair;
 866         while (pairSearch.findNextPair(&pair))
 867         {
 868             if(CalculateAtomicDistances(
 869                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 870                 < minimalCAdistance){
 871                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 872                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 873                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 874                 }
 875             }
 876         }
 877
 878         break;
 879     }
 880     case (NBSearchMethod::Experimental): { // TODO FIX
 881
 882         alternateNeighborhoodSearch as_;
 883
 884         as_.setCutoff(initParams.cutoff_);
 885
 886         as_.AltPairSearch(fr, IndexMap);
 887
 888         while (as_.findNextPair()){
 889             if(CalculateAtomicDistances(
 890                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 891                 < minimalCAdistance){
 892                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 893                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 894                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 895                 }
 896             }
 897         }
 898
 899         break;
 900     }
 901     default: {
 902
 903         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 904             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 905                 if(CalculateAtomicDistances(
 906                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 907                     < minimalCAdistance){
 908                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 909                     if (Acceptor != Donor + 1){
 910                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 911                     }
 912                 }
 913             }
 914         }
 915         break;
 916     }
 917     }
 918
 919
 920 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 921 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 922 //    }
 923
 924    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 925    calculateBends(fr, pbc);
 926    Storage.storageData(frnr, PatternSearch.patternSearch());
 927
 928 }
 929
 930 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 931     return Storage.returnData();
 932 }
 933
 934 } // namespace analysismodules
 935
 936 } // namespace gmx