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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  17 * Lesser General Public License for more details.
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  34 */
  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 }
  98
  99 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
 100     TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
 101 }
 102
 103 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
 104     return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
 105 }
 106
 107 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
 108     return breakPartners[0] == partner || breakPartners[1] == partner;
 109 }
 110
 111 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
 112     return TurnsStatusArray[static_cast<std::size_t>(turn)];
 113 }
 114
 115 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
 116     if (breakPartners[0] == nullptr){
 117         breakPartners[0] = breakPartner;
 118     }
 119     else{
 120         breakPartners[1] = breakPartner;
 121     }
 122     setStatus(secondaryStructureTypes::Break);
 123 }
 124
 125 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{ // prob should add resi name comparison ?
 126     if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
 127         (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
 128         (*ResInfoMap)[Acceptor].info == nullptr ){
 129         std::cout << "Bad hbond check. Reason(s): " ;
 130         if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 131             std::cout << "Donor has no acceptor[0]; ";
 132         }
 133         if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 134             std::cout << "Donor has no acceptor[1]; ";
 135         }
 136         if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 137             std::cout << "No info about acceptor; ";
 138         }
 139         std::cout << std::endl;
 140         return false;
 141     }
 142     else {
 143         std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": ";
 144         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;
 145         std::cout << "DONOR's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
 146         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;
 147         std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
 148         if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 149                 ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 150             std::cout << "HBond Exist" << std::endl;
 151         }
 152     }
 153
 154     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 155            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 156
 157
 158 }
 159
 160 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 161     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 162     if ( i > j ){
 163         std::swap(i, j);
 164     }
 165
 166     for (; i != j; ++i){
 167         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 168             std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 169             return false;
 170         }
 171     }
 172     return true;
 173 }
 174
 175 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 176     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
 177         return bridgeTypes::None;
 178     }
 179     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
 180         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
 181             return bridgeTypes::ParallelBridge;
 182         }
 183         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
 184             return bridgeTypes::AntiParallelBridge;
 185         }
 186     }
 187     return bridgeTypes::None;
 188 }
 189
 190 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 191     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 192         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 193             bridgeTypes type {calculateBridge(i, j)};
 194             if (type == bridgeTypes::None){
 195                 continue;
 196             }
 197             bool found {false};
 198         }
 199     }
 200
 201
 202
 203
 204
 205
 206
 207
 208
 209
 210
 211
 212 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 213 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 214 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 215 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 216 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 217 //                    Bridge[i].push_back(j);
 218 //                }
 219 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 220 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 221 //                    AntiBridge[i].push_back(j);
 222 //                }
 223 //            }
 224 //        }
 225 //    }
 226 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 227 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 228 //            setStatus(i, secondaryStructureTypes::Bulge);
 229 //        }
 230 //    }
 231 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 232 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 233 //            if (j == i){
 234 //                continue;
 235 //            }
 236 //            else {
 237 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 238 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 239 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 240 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 241 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 242 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 243 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 244 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 245 //                                        < 5)){
 246 //                                    if (j < i){
 247 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 248 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 249 //                                        }
 250 //                                    }
 251 //                                    else{
 252 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 253 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 254 //                                        }
 255 //                                    }
 256 //                                }
 257 //                            }
 258 //                        }
 259 //                    }
 260 //                }
 261 //            }
 262 //        }
 263 //    }
 264 }
 265
 266 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 267     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 268         std::size_t stride {static_cast<std::size_t>(i) + 3};
 269         std::cout << "Testing Helix_" << stride << std::endl;
 270         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 271             std::cout << "Testing " << j << " and " << j + stride << std::endl;
 272             if ( hasHBondBetween(j, j + stride) && NoChainBreaksBetween(j, j + stride) ){
 273                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 274                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 275
 276                 for (std::size_t k {1}; k < stride; ++k){
 277                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 278                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 279                         SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 280                     }
 281
 282                 }
 283
 284                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 285                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 286                 }
 287                 else {
 288                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 289                 }
 290             }
 291         }
 292     }
 293
 294     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 295         std::size_t stride {static_cast<std::size_t>(i) + 3};
 296         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 297             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 298                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 299                 bool empty = true;
 300                 secondaryStructureTypes Helix;
 301                 switch(i){
 302                 case turnsTypes::Turn_3:
 303                     for (std::size_t k {0}; empty && k < stride; ++k){
 304                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 305                     }
 306                     Helix = secondaryStructureTypes::Helix_3;
 307                     break;
 308                 case turnsTypes::Turn_5:
 309                     for (std::size_t k {0}; empty && k < stride; ++k){
 310                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 311                     }
 312                     Helix = secondaryStructureTypes::Helix_5;
 313                     break;
 314                 default:
 315                     Helix = secondaryStructureTypes::Helix_4;
 316                     break;
 317                 }
 318                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 319                     for(std::size_t k {0}; k < stride - 1; ++k ){
 320                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 321                     }
 322                 }
 323             }
 324         }
 325     }
 326
 327 //    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 328 //        if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
 329 //            bool isTurn = false;
 330 //            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 331 //                std::size_t stride {static_cast<std::size_t>(i) + 3};
 332 //                for(std::size_t k {1}; k < stride; ++k){
 333 //                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 334 //                }
 335 //            }
 336
 337 //            if (isTurn){
 338 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 339 //            }
 340 //            else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 341 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 342 //            }
 343 //        }
 344 //    }
 345
 346 }
 347
 348 void secondaryStructures::analyzePPHelicesPatterns(){}
 349
 350 std::string secondaryStructures::patternSearch(){
 351
 352
 353 //    analyzeBridgesAndLaddersPatterns();
 354     analyzeTurnsAndHelicesPatterns();
 355 //    analyzePPHelicesPatterns();
 356
 357 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 358 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 359 //    }
 360
 361 //    std::cout.precision(5);
 362 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 363 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 364 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 365 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 366 //        }
 367 //        else {
 368 //            std::cout << " has no donor[0] and" ;
 369 //        }
 370 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 371 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 372 //        }
 373 //        else {
 374 //            std::cout << " has no acceptor[0]" ;
 375 //        }
 376 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 377 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 378 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 379 //        }
 380 //        else {
 381 //            std::cout << " has no donor[1] and" ;
 382 //        }
 383 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 384 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 385 //        }
 386 //        else {
 387 //            std::cout << " has no acceptor[1]" ;
 388 //        }
 389 //    }
 390
 391     /*Write Data*/
 392
 393     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 394         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 395             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 396                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 397             }
 398         }
 399     }
 400
 401     /*Add breaks*/
 402
 403     if(SecondaryStructuresStatusMap.size() > 1){
 404         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 405             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 406                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 407                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 408                     ++linefactor;
 409                 }
 410             }
 411         }
 412     }
 413     return SecondaryStructuresStringLine;
 414 }
 415
 416 secondaryStructures::~secondaryStructures(){
 417     SecondaryStructuresStatusMap.resize(0);
 418     SecondaryStructuresStringLine.resize(0);
 419 }
 420
 421 DsspTool::DsspStorage::DsspStorage(){
 422     storaged_data.resize(0);
 423 }
 424
 425 void DsspTool::DsspStorage::clearAll(){
 426     storaged_data.resize(0);
 427 }
 428
 429 std::mutex DsspTool::DsspStorage::mx;
 430
 431 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 432     std::lock_guard<std::mutex> guardian(mx);
 433     std::pair<int, std::string> datapair(frnr, data);
 434     storaged_data.push_back(datapair);
 435 }
 436
 437 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 438     std::sort(storaged_data.begin(), storaged_data.end());
 439     return storaged_data;
 440 }
 441
 442 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 443     cutoff = cutoff_init;
 444 }
 445
 446 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 447     while (coordinate < 0) {
 448         coordinate += vector_length;
 449     }
 450     while (coordinate >= vector_length) {
 451         coordinate -= vector_length;
 452     }
 453 }
 454
 455 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 456     if (x < 0) {
 457         x += x_max;
 458     }
 459     if (x >= x_max) {
 460         x -= x_max;
 461     }
 462 }
 463
 464 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 465     rvec coordinates, box_vector_length;
 466     num_of_miniboxes.resize(0);
 467     num_of_miniboxes.resize(3);
 468     for (std::size_t i{XX}; i <= ZZ; ++i) {
 469         box_vector_length[i] = std::sqrt(
 470                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 471         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 472     }
 473     MiniBoxesMap.resize(0);
 474     MiniBoxesReverseMap.resize(0);
 475     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 476                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 477                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 478                              0))));
 479     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 480     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 481         for (std::size_t j{XX}; j <= ZZ; ++j) {
 482             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 483             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 484         }
 485         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 486                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 487         for (std::size_t j{XX}; j <= ZZ; ++j){
 488             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 489         }
 490     }
 491 }
 492
 493 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 494     GetMiniBoxesMap(fr, IndexMap);
 495     MiniBoxSize[XX] = MiniBoxesMap.size();
 496     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 497     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 498     PairMap.resize(0);
 499     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 500     ResiI = PairMap.begin();
 501     ResiJ = ResiI->begin();
 502
 503     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 504         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 505             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 506                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 507                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 508                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 509                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 510                     }
 511                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 512                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 513                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 514                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 515                         }
 516                     }
 517                 }
 518             }
 519         }
 520     }
 521 }
 522
 523 bool alternateNeighborhoodSearch::findNextPair(){
 524
 525     if(!PairMap.size()){
 526         return false;
 527     }
 528
 529     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 530         for(; ResiJ != ResiI->end(); ++ResiJ){
 531             if(*ResiJ){
 532                 resiIpos = ResiI - PairMap.begin();
 533                 resiJpos = ResiJ - ResiI->begin();
 534                 if ( ResiJ != ResiI->end() ){
 535                     ++ResiJ;
 536                 }
 537                 else if (ResiI != PairMap.end()) {
 538                     ++ResiI;
 539                     ResiJ = ResiI->begin();
 540                 }
 541                 else {
 542                     return false; // ???
 543                 }
 544                 return true;
 545             }
 546         }
 547     }
 548
 549     return false;
 550 }
 551
 552 std::size_t alternateNeighborhoodSearch::getResiI() const {
 553     return resiIpos;
 554 }
 555
 556 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 557     return resiJpos;
 558 }
 559
 560
 561 DsspTool::DsspStorage DsspTool::Storage;
 562
 563 DsspTool::DsspTool(){
 564 }
 565
 566 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 567 {
 568    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 569    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 570    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 571    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 572    {
 573        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 574                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 575                                     fr,
 576                                     pbc)
 577            > maxdist)
 578        {
 579            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 580            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 581
 582 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 583        }
 584    }
 585    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 586    {
 587        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 588            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 589            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 590            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 591           )
 592        {
 593            continue;
 594        }
 595        for (int j{ 0 }; j < 3; ++j)
 596        {
 597            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 598                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 599            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 600                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 601        }
 602        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 603        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 604                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 605                                         fr,
 606                                         pbc)
 607                * gmx::c_angstrom / gmx::c_nano
 608                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 609                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 610                                           fr,
 611                                           pbc)
 612                * gmx::c_angstrom / gmx::c_nano;
 613        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 614        if (degree > benddegree)
 615        {
 616            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 617        }
 618    }
 619 }
 620
 621 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 622                        ResInfo& Acceptor,
 623                        const t_trxframe&          fr,
 624                        const t_pbc*               pbc)
 625 {
 626    /*
 627     * DSSP uses eq from dssp 2.x
 628     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 629     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 630     * if R is in A
 631     * Hbond if E < -0.5
 632     *
 633     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 634     *
 635     */
 636
 637     if (CalculateAtomicDistances(
 638                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 639         >= minimalCAdistance)
 640     {
 641         return void();
 642     }
 643
 644     const float kCouplingConstant = 27.888;
 645     const float minimalAtomDistance{ 0.5 },
 646             minEnergy{ -9.9 };
 647     float HbondEnergy{ 0 };
 648     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 649
 650 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 651
 652     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 653                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 654         distanceNO = CalculateAtomicDistances(
 655                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 656         distanceNC = CalculateAtomicDistances(
 657                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 658         if (initParams.addHydrogens){
 659             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 660                rvec atomH{};
 661                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 662                for (int i{XX}; i <= ZZ; ++i){
 663                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 664                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 665                    atomH[i] += prevCO / prevCODist;
 666                }
 667                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 668                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 669             }
 670             else{
 671                 distanceHO = distanceNO;
 672                 distanceHC = distanceNC;
 673             }
 674        }
 675        else {
 676            distanceHO = CalculateAtomicDistances(
 677                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 678            distanceHC = CalculateAtomicDistances(
 679                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 680        }
 681        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 682         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 683        {
 684             HbondEnergy = minEnergy;
 685        }
 686        else{
 687            HbondEnergy =
 688                    kCouplingConstant
 689                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 690        }
 691
 692 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 693 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 694 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 695 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 696 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 697 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 698
 699        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 700
 701        if ( HbondEnergy < minEnergy ){
 702             HbondEnergy = minEnergy;
 703        }
 704
 705 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 706     }
 707 //    else{
 708 //        std::cout << "Donor Is Proline" << std::endl;
 709 //    }
 710
 711     if (HbondEnergy < Donor.acceptorEnergy[0]){
 712            Donor.acceptor[1] = Donor.acceptor[0];
 713            Donor.acceptor[0] = Acceptor.info;
 714            Donor.acceptorEnergy[0] = HbondEnergy;
 715     }
 716     else if (HbondEnergy < Donor.acceptorEnergy[1]){
 717            Donor.acceptor[1] = Acceptor.info;
 718            Donor.acceptorEnergy[1] = HbondEnergy;
 719     }
 720
 721     if (HbondEnergy < Acceptor.donorEnergy[0]){
 722            Acceptor.donor[1] = Acceptor.donor[0];
 723            Acceptor.donor[0] = Donor.info;
 724            Acceptor.donorEnergy[0] = HbondEnergy;
 725     }
 726     else if (HbondEnergy < Acceptor.donorEnergy[1]){
 727            Acceptor.donor[1] = Donor.info;
 728            Acceptor.donorEnergy[1] = HbondEnergy;
 729     }
 730 }
 731
 732
 733 /* Calculate Distance From B to A */
 734 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 735 {
 736    gmx::RVec r{ 0, 0, 0 };
 737    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 738    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 739 }
 740
 741 /* Calculate Distance From B to A, where A is only fake coordinates */
 742 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 743 {
 744    gmx::RVec r{ 0, 0, 0 };
 745    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 746    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 747 }
 748
 749 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 750 {
 751    initParams = initParamz;
 752    ResInfo _backboneAtoms;
 753    std::size_t                 i{ 0 };
 754    std::string proLINE;
 755    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
 756    IndexMap.resize(0);
 757    IndexMap.push_back(_backboneAtoms);
 758    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 759    proLINE = *(IndexMap[i].info->name);
 760    if( proLINE.compare("PRO") == 0 ){
 761        IndexMap[i].is_proline = true;
 762    }
 763
 764    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
 765        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
 766        {
 767            ++i;
 768            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
 769            IndexMap.emplace_back(_backboneAtoms);
 770            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 771            proLINE = *(IndexMap[i].info->name);
 772            if( proLINE.compare("PRO") == 0 ){
 773                IndexMap[i].is_proline = true;
 774            }
 775
 776        }
 777        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
 778        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
 779        {
 780            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
 781        }
 782        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
 783        {
 784            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
 785        }
 786        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
 787        {
 788            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
 789        }
 790        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
 791        {
 792            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
 793            if (initParamz.addHydrogens == true){
 794                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 795            }
 796        }
 797        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 798        {
 799            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 800        }
 801
 802
 803
 804 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 805 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 806 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 807 //       }
 808    }
 809
 810    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 811        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 812
 813        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 814
 815 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 816 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 817 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 818 //         std::cout << IndexMap[j].prevResi->info->nr;
 819 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 820 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 821 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 822 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 823 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 824 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 825    }
 826
 827    nres = i + 1;
 828 }
 829
 830 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 831 {
 832
 833     switch(initParams.NBS){
 834     case (NBSearchMethod::Classique): {
 835
 836         // store positions of CA atoms to use them for nbSearch
 837         std::vector<gmx::RVec> positionsCA_;
 838         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 839         {
 840             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 841         }
 842
 843         AnalysisNeighborhood nb_;
 844         nb_.setCutoff(initParams.cutoff_);
 845         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 846         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 847         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 848         gmx::AnalysisNeighborhoodPair       pair;
 849         while (pairSearch.findNextPair(&pair))
 850         {
 851             if(CalculateAtomicDistances(
 852                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 853                 < minimalCAdistance){
 854                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 855                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 856                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 857                 }
 858             }
 859         }
 860
 861         break;
 862     }
 863     case (NBSearchMethod::Experimental): { // TODO FIX
 864
 865         alternateNeighborhoodSearch as_;
 866
 867         as_.setCutoff(initParams.cutoff_);
 868
 869         as_.AltPairSearch(fr, IndexMap);
 870
 871         while (as_.findNextPair()){
 872             if(CalculateAtomicDistances(
 873                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 874                 < minimalCAdistance){
 875                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 876                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 877                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 878                 }
 879             }
 880         }
 881
 882         break;
 883     }
 884     default: {
 885
 886         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 887             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 888                 if(CalculateAtomicDistances(
 889                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 890                     < minimalCAdistance){
 891                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 892                     if (Acceptor != Donor + 1){
 893                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 894                     }
 895                 }
 896             }
 897         }
 898         break;
 899     }
 900     }
 901
 902
 903 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 904 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 905 //    }
 906
 907    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 908    calculateBends(fr, pbc);
 909    Storage.storageData(frnr, PatternSearch.patternSearch());
 910
 911 }
 912
 913 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 914     return Storage.returnData();
 915 }
 916
 917 } // namespace analysismodules
 918
 919 } // namespace gmx