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 *
  14 * GROMACS is distributed in the hope that it will be useful,
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  16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  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 of the last residue
  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         return false;
 130     }
 131     else {
 132
 133 //        std::cout << "Comparing DONOR " << Donor << " And ACCEPTOR " << Acceptor << " :";
 134 //        std::cout << "DONOR's acceptor adresses are " << (*ResInfoMap)[Donor].acceptor[0] << ", " << (*ResInfoMap)[Donor].acceptor[1] << " and ACCEPTOR adress is " << (*ResInfoMap)[Acceptor].info << std::endl;
 135 //        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;
 136 //        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;
 137
 138 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 139 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 140 //            std::cout << "HBond Exist" << std::endl;
 141 //        }
 142         return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 143                 ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 144     }
 145 }
 146
 147 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 148     bool flag{true};
 149     std::size_t i{Resi1}, j{Resi2}; // From i to j
 150     if ( Resi2 < Resi1){
 151         std::swap(i, j);
 152     }
 153
 154     for (; i != j; ++i){
 155         flag = !(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]));
 156     }
 157
 158     if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 159         std::cout << " SASSA " << std::endl;
 160     }
 161
 162     if (!flag){
 163         std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 164     }
 165
 166     return flag;
 167 }
 168
 169 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 170     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
 171         return bridgeTypes::None;
 172     }
 173     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
 174         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
 175             return bridgeTypes::ParallelBridge;
 176         }
 177         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
 178             return bridgeTypes::AntiParallelBridge;
 179         }
 180     }
 181     return bridgeTypes::None;
 182 }
 183
 184 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 185     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 186         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 187             bridgeTypes type {calculateBridge(i, j)};
 188             if (type == bridgeTypes::None){
 189                 continue;
 190             }
 191             bool found {false};
 192         }
 193     }
 194
 195
 196
 197
 198
 199
 200
 201
 202
 203
 204
 205
 206 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 207 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 208 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 209 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 210 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 211 //                    Bridge[i].push_back(j);
 212 //                }
 213 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 214 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 215 //                    AntiBridge[i].push_back(j);
 216 //                }
 217 //            }
 218 //        }
 219 //    }
 220 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 221 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 222 //            setStatus(i, secondaryStructureTypes::Bulge);
 223 //        }
 224 //    }
 225 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 226 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 227 //            if (j == i){
 228 //                continue;
 229 //            }
 230 //            else {
 231 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 232 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 233 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 234 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 235 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 236 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 237 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 238 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 239 //                                        < 5)){
 240 //                                    if (j < i){
 241 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 242 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 243 //                                        }
 244 //                                    }
 245 //                                    else{
 246 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 247 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 248 //                                        }
 249 //                                    }
 250 //                                }
 251 //                            }
 252 //                        }
 253 //                    }
 254 //                }
 255 //            }
 256 //        }
 257 //    }
 258 }
 259
 260 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 261     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 262         std::cout << "Testing Helix_" << static_cast<std::size_t>(i) + 3 << std::endl;
 263         std::size_t stride {static_cast<std::size_t>(i) + 3};
 264         for(std::size_t j {0}; j + static_cast<std::size_t>(i) < SecondaryStructuresStatusMap.size(); ++j){
 265             std::cout << "Testing " << j << " and " << j + stride << std::endl;
 266             if ( hasHBondBetween(j, j + (static_cast<std::size_t>(i))) && NoChainBreaksBetween(j, j + stride) ){
 267                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 268                 SecondaryStructuresStatusMap[j + static_cast<std::size_t>(i)].setStatus(HelixPositions::End, i);
 269
 270                 for (std::size_t k {1}; k < (static_cast<std::size_t>(i)); ++k){
 271                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 272                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 273                     }
 274
 275                 }
 276
 277                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 278                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 279                 }
 280                 else {
 281                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 282                 }
 283             }
 284         }
 285     }
 286
 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         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 290             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 291                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 292                 bool empty = true;
 293                 secondaryStructureTypes Helix;
 294                 switch(i){
 295                 case turnsTypes::Turn_3:
 296                     for (std::size_t k {0}; empty && k < stride; ++k){
 297                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 298                     }
 299                     Helix = secondaryStructureTypes::Helix_3;
 300                     break;
 301                 case turnsTypes::Turn_5:
 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_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5));
 304                     }
 305                     Helix = secondaryStructureTypes::Helix_4;
 306                     break;
 307                 default:
 308                     Helix = secondaryStructureTypes::Helix_4;
 309                     break;
 310                 }
 311                 std::cout << j << " is HELIX" << std::endl;
 312                 if ( empty ){
 313                     for(std::size_t k {0}; k < (static_cast<std::size_t>(i)); ++k ){
 314                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 315                     }
 316                 }
 317             }
 318         }
 319     }
 320
 321     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 322         if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
 323             bool isTurn = false;
 324             for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 325                 std::size_t stride {static_cast<std::size_t>(i) + 3};
 326                 for(std::size_t k {1}; k < stride; ++k){
 327                     isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 328                 }
 329             }
 330
 331             if (isTurn){
 332                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 333             }
 334             else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 335                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 336             }
 337         }
 338     }
 339
 340 }
 341
 342 void secondaryStructures::analyzePPHelicesPatterns(){}
 343
 344 std::string secondaryStructures::patternSearch(){
 345
 346 //    analyzeBridgesAndLaddersPatterns();
 347     analyzeTurnsAndHelicesPatterns();
 348 //    analyzePPHelicesPatterns();
 349
 350 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 351 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 352 //    }
 353
 354 //    std::cout.precision(5);
 355 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 356 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 357 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 358 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 359 //        }
 360 //        else {
 361 //            std::cout << " has no donor[0] and" ;
 362 //        }
 363 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 364 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 365 //        }
 366 //        else {
 367 //            std::cout << " has no acceptor[0]" ;
 368 //        }
 369 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 370 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 371 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 372 //        }
 373 //        else {
 374 //            std::cout << " has no donor[1] and" ;
 375 //        }
 376 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 377 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 378 //        }
 379 //        else {
 380 //            std::cout << " has no acceptor[1]" ;
 381 //        }
 382 //    }
 383
 384     /*Write Data*/
 385
 386     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 387         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 388             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 389                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 390             }
 391         }
 392     }
 393
 394     /*Add breaks*/
 395
 396     if(SecondaryStructuresStatusMap.size() > 1){
 397         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 398             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 399                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 400                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 401                     ++linefactor;
 402                 }
 403             }
 404         }
 405     }
 406     return SecondaryStructuresStringLine;
 407 }
 408
 409 secondaryStructures::~secondaryStructures(){
 410     SecondaryStructuresStatusMap.resize(0);
 411     SecondaryStructuresStringLine.resize(0);
 412 }
 413
 414 DsspTool::DsspStorage::DsspStorage(){
 415     storaged_data.resize(0);
 416 }
 417
 418 void DsspTool::DsspStorage::clearAll(){
 419     storaged_data.resize(0);
 420 }
 421
 422 std::mutex DsspTool::DsspStorage::mx;
 423
 424 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 425     std::lock_guard<std::mutex> guardian(mx);
 426     std::pair<int, std::string> datapair(frnr, data);
 427     storaged_data.push_back(datapair);
 428 }
 429
 430 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 431     std::sort(storaged_data.begin(), storaged_data.end());
 432     return storaged_data;
 433 }
 434
 435 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 436     cutoff = cutoff_init;
 437 }
 438
 439 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 440     while (coordinate < 0) {
 441         coordinate += vector_length;
 442     }
 443     while (coordinate >= vector_length) {
 444         coordinate -= vector_length;
 445     }
 446 }
 447
 448 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 449     if (x < 0) {
 450         x += x_max;
 451     }
 452     if (x >= x_max) {
 453         x -= x_max;
 454     }
 455 }
 456
 457 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 458     rvec coordinates, box_vector_length;
 459     num_of_miniboxes.resize(0);
 460     num_of_miniboxes.resize(3);
 461     for (std::size_t i{XX}; i <= ZZ; ++i) {
 462         box_vector_length[i] = std::sqrt(
 463                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 464         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 465     }
 466     MiniBoxesMap.resize(0);
 467     MiniBoxesReverseMap.resize(0);
 468     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 469                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 470                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 471                              0))));
 472     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 473     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 474         for (std::size_t j{XX}; j <= ZZ; ++j) {
 475             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 476             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 477         }
 478         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 479                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 480         for (std::size_t j{XX}; j <= ZZ; ++j){
 481             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 482         }
 483     }
 484 }
 485
 486 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 487     GetMiniBoxesMap(fr, IndexMap);
 488     MiniBoxSize[XX] = MiniBoxesMap.size();
 489     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 490     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 491     PairMap.resize(0);
 492     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 493     ResiI = PairMap.begin();
 494     ResiJ = ResiI->begin();
 495
 496     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 497         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 498             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 499                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 500                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 501                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 502                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 503                     }
 504                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 505                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 506                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 507                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 508                         }
 509                     }
 510                 }
 511             }
 512         }
 513     }
 514 }
 515
 516 bool alternateNeighborhoodSearch::findNextPair(){
 517
 518     if(!PairMap.size()){
 519         return false;
 520     }
 521
 522     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 523         for(; ResiJ != ResiI->end(); ++ResiJ){
 524             if(*ResiJ){
 525                 resiIpos = ResiI - PairMap.begin();
 526                 resiJpos = ResiJ - ResiI->begin();
 527                 if ( ResiJ != ResiI->end() ){
 528                     ++ResiJ;
 529                 }
 530                 else if (ResiI != PairMap.end()) {
 531                     ++ResiI;
 532                     ResiJ = ResiI->begin();
 533                 }
 534                 else {
 535                     return false; // ???
 536                 }
 537                 return true;
 538             }
 539         }
 540     }
 541
 542     return false;
 543 }
 544
 545 std::size_t alternateNeighborhoodSearch::getResiI() const {
 546     return resiIpos;
 547 }
 548
 549 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 550     return resiJpos;
 551 }
 552
 553
 554 DsspTool::DsspStorage DsspTool::Storage;
 555
 556 DsspTool::DsspTool(){
 557 }
 558
 559 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 560 {
 561    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 562    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 563    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 564    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 565    {
 566        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 567                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 568                                     fr,
 569                                     pbc)
 570            > maxdist)
 571        {
 572            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 573            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 574
 575 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 576        }
 577    }
 578    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 579    {
 580        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 581            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 582            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 583            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 584           )
 585        {
 586            continue;
 587        }
 588        for (int j{ 0 }; j < 3; ++j)
 589        {
 590            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 591                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 592            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 593                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 594        }
 595        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 596        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 597                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 598                                         fr,
 599                                         pbc)
 600                * gmx::c_angstrom / gmx::c_nano
 601                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 602                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 603                                           fr,
 604                                           pbc)
 605                * gmx::c_angstrom / gmx::c_nano;
 606        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 607        if (degree > benddegree)
 608        {
 609            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 610        }
 611    }
 612 }
 613
 614 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 615                        ResInfo& Acceptor,
 616                        const t_trxframe&          fr,
 617                        const t_pbc*               pbc)
 618 {
 619    /*
 620     * DSSP uses eq from dssp 2.x
 621     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 622     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 623     * if R is in A
 624     * Hbond if E < -0.5
 625     */
 626
 627     const float kCouplingConstant = 27.888;
 628     const float minimalAtomDistance{ 0.5 },
 629             minEnergy{ -9.9 };
 630     float HbondEnergy{ 0 };
 631     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 632
 633    if( !(Donor.is_proline) ){
 634        if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 635            && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )  // Kinda ew
 636        {
 637
 638            distanceNO = CalculateAtomicDistances(
 639                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 640            distanceNC = CalculateAtomicDistances(
 641                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 642
 643            if (initParams.addHydrogens){
 644                if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 645 //                   std::cout << "On donor " << Donor.info->nr << *(Donor.info->name) << std::endl;
 646 //                   std::cout << "Prev donor is " << Donor.prevResi->info->nr << *(Donor.prevResi->info->name) << std::endl;
 647 //                   std::cout << "Prev C index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomC) << std::endl;
 648 //                   std::cout << "Prev O index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomO) << std::endl;
 649                    rvec atomH{};
 650                    float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 651                    for (int i{XX}; i <= ZZ; ++i){
 652                        float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 653                        atomH[i] = prevCO / prevCODist;
 654                    }
 655                    distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 656                    distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 657                }
 658                else{
 659                    distanceHO = distanceNO;
 660                    distanceHC = distanceNC;
 661                }
 662            }
 663            else {
 664                distanceHO = CalculateAtomicDistances(
 665                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 666                distanceHC = CalculateAtomicDistances(
 667                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 668            }
 669
 670            if (CalculateAtomicDistances(
 671                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 672                < minimalCAdistance)
 673            {
 674                if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 675                    || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 676                {
 677                    HbondEnergy = minEnergy;
 678
 679 //                   std::cout << "HBOND exists cause of distance" << std::endl;
 680                }
 681                else
 682                {
 683                    HbondEnergy =
 684                            kCouplingConstant
 685                            * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 686                    HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 687
 688 //                   std::cout.precision(5);
 689 //                   std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
 690
 691 //                   if ( HbondEnergy == 0){
 692 //                       std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
 693 //                   }
 694
 695                    if ( HbondEnergy < minEnergy ){
 696                        HbondEnergy = minEnergy;
 697                    }
 698                }
 699            }
 700        }
 701    }
 702 //   else {
 703 //       std::cerr << "PRO DETECTED! THIS IS RESI № " << Donor.info->nr << std::endl; //IT WORKS JUST FINE
 704 //   }
 705
 706    if (HbondEnergy < Donor.acceptorEnergy[0]){
 707        Donor.acceptor[1] = Donor.acceptor[0];
 708        Donor.acceptor[0] = Acceptor.info;
 709        Donor.acceptorEnergy[0] = HbondEnergy;
 710    }
 711    else if (HbondEnergy < Donor.acceptorEnergy[1]){
 712        Donor.acceptor[1] = Acceptor.info;
 713        Donor.acceptorEnergy[1] = HbondEnergy;
 714    }
 715
 716    if (HbondEnergy < Acceptor.donorEnergy[0]){
 717        Acceptor.donor[1] = Acceptor.donor[0];
 718        Acceptor.donor[0] = Donor.info;
 719        Acceptor.donorEnergy[0] = HbondEnergy;
 720    }
 721    else if (HbondEnergy < Acceptor.donorEnergy[1]){
 722        Acceptor.donor[1] = Donor.info;
 723        Acceptor.donorEnergy[1] = HbondEnergy;
 724    }
 725 }
 726
 727
 728 /* Calculate Distance From B to A */
 729 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 730 {
 731    gmx::RVec r{ 0, 0, 0 };
 732    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 733 //   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
 734    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 735 }
 736
 737 /* Calculate Distance From B to A, where A is only fake coordinates */
 738 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 739 {
 740    gmx::RVec r{ 0, 0, 0 };
 741    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 742 //   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
 743    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 744 }
 745
 746 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 747 {
 748
 749    std::cout << "Init started" << std::endl;
 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        }
 793        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 794        {
 795            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 796        }
 797
 798 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 799 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 800 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 801 //       }
 802    }
 803
 804    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 805        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 806
 807        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 808
 809 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 810 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 811 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 812 //         std::cout << IndexMap[j].prevResi->info->nr;
 813 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 814 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 815 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 816 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 817 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 818 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 819    }
 820
 821    nres = i + 1;
 822 }
 823
 824 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 825 {
 826
 827     switch(initParams.NBS){
 828     case (NBSearchMethod::Classique): {
 829
 830         // store positions of CA atoms to use them for nbSearch
 831         std::vector<gmx::RVec> positionsCA_;
 832         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 833         {
 834             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 835         }
 836
 837         AnalysisNeighborhood nb_;
 838         nb_.setCutoff(initParams.cutoff_);
 839         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 840         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 841         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 842         gmx::AnalysisNeighborhoodPair       pair;
 843         while (pairSearch.findNextPair(&pair))
 844         {
 845             if(CalculateAtomicDistances(
 846                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 847                 < minimalCAdistance){
 848                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 849                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 850                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 851                 }
 852             }
 853         }
 854
 855         break;
 856     }
 857     case (NBSearchMethod::Experimental): { // TODO FIX
 858
 859         alternateNeighborhoodSearch as_;
 860
 861         as_.setCutoff(initParams.cutoff_);
 862
 863         as_.AltPairSearch(fr, IndexMap);
 864
 865         while (as_.findNextPair()){
 866             if(CalculateAtomicDistances(
 867                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 868                 < minimalCAdistance){
 869                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 870                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 871                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 872                 }
 873             }
 874         }
 875
 876         break;
 877     }
 878     default: {
 879
 880         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 881             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 882                 if(CalculateAtomicDistances(
 883                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 884                     < minimalCAdistance){
 885                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 886                     if (Acceptor != Donor + 1){
 887                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 888                     }
 889                 }
 890             };
 891         };
 892         break;
 893     }
 894     }
 895
 896
 897 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 898 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 899 //    }
 900
 901    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 902    calculateBends(fr, pbc);
 903    Storage.storageData(frnr, PatternSearch.patternSearch());
 904
 905 }
 906
 907 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 908     return Storage.returnData();
 909 }
 910
 911 } // namespace analysismodules
 912
 913 } // namespace gmx