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