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