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