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 → i <= j
 150     if ( i > j ){
 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 (!flag){
 159         std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 160     }
 161
 162     return flag;
 163 }
 164
 165 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 166     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
 167         return bridgeTypes::None;
 168     }
 169     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
 170         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
 171             return bridgeTypes::ParallelBridge;
 172         }
 173         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
 174             return bridgeTypes::AntiParallelBridge;
 175         }
 176     }
 177     return bridgeTypes::None;
 178 }
 179
 180 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 181     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 182         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 183             bridgeTypes type {calculateBridge(i, j)};
 184             if (type == bridgeTypes::None){
 185                 continue;
 186             }
 187             bool found {false};
 188         }
 189     }
 190
 191
 192
 193
 194
 195
 196
 197
 198
 199
 200
 201
 202 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 203 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 204 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 205 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 206 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 207 //                    Bridge[i].push_back(j);
 208 //                }
 209 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 210 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 211 //                    AntiBridge[i].push_back(j);
 212 //                }
 213 //            }
 214 //        }
 215 //    }
 216 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 217 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 218 //            setStatus(i, secondaryStructureTypes::Bulge);
 219 //        }
 220 //    }
 221 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 222 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 223 //            if (j == i){
 224 //                continue;
 225 //            }
 226 //            else {
 227 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 228 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 229 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 230 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 231 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 232 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 233 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 234 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 235 //                                        < 5)){
 236 //                                    if (j < i){
 237 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 238 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 239 //                                        }
 240 //                                    }
 241 //                                    else{
 242 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 243 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 244 //                                        }
 245 //                                    }
 246 //                                }
 247 //                            }
 248 //                        }
 249 //                    }
 250 //                }
 251 //            }
 252 //        }
 253 //    }
 254 }
 255
 256 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 257     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 258         std::cout << "Testing Helix_" << static_cast<std::size_t>(i) + 3 << std::endl;
 259         std::size_t stride {static_cast<std::size_t>(i) + 3};
 260         for(std::size_t j {0}; j + static_cast<std::size_t>(i) < SecondaryStructuresStatusMap.size(); ++j){
 261             std::cout << "Testing " << j << " and " << j + stride << std::endl;
 262             if ( hasHBondBetween(j, j + (static_cast<std::size_t>(i))) && NoChainBreaksBetween(j, j + stride) ){
 263                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 264                 SecondaryStructuresStatusMap[j + static_cast<std::size_t>(i)].setStatus(HelixPositions::End, i);
 265
 266                 for (std::size_t k {1}; k < (static_cast<std::size_t>(i)); ++k){
 267                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 268                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 269                     }
 270
 271                 }
 272
 273                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 274                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 275                 }
 276                 else {
 277                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 278                 }
 279             }
 280         }
 281     }
 282
 283     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 284         std::size_t stride {static_cast<std::size_t>(i) + 3};
 285         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 286             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 287                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 288                 bool empty = true;
 289                 secondaryStructureTypes Helix;
 290                 switch(i){
 291                 case turnsTypes::Turn_3:
 292                     for (std::size_t k {0}; empty && k < stride; ++k){
 293                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 294                     }
 295                     Helix = secondaryStructureTypes::Helix_3;
 296                     break;
 297                 case turnsTypes::Turn_5:
 298                     for (std::size_t k {0}; empty && k < stride; ++k){
 299                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5));
 300                     }
 301                     Helix = secondaryStructureTypes::Helix_4;
 302                     break;
 303                 default:
 304                     Helix = secondaryStructureTypes::Helix_4;
 305                     break;
 306                 }
 307                 std::cout << j << " is HELIX" << std::endl;
 308                 if ( empty ){
 309                     for(std::size_t k {0}; k < (static_cast<std::size_t>(i)); ++k ){
 310                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 311                     }
 312                 }
 313             }
 314         }
 315     }
 316
 317     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 318         if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
 319             bool isTurn = false;
 320             for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 321                 std::size_t stride {static_cast<std::size_t>(i) + 3};
 322                 for(std::size_t k {1}; k < stride; ++k){
 323                     isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 324                 }
 325             }
 326
 327             if (isTurn){
 328                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 329             }
 330             else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 331                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 332             }
 333         }
 334     }
 335
 336 }
 337
 338 void secondaryStructures::analyzePPHelicesPatterns(){}
 339
 340 std::string secondaryStructures::patternSearch(){
 341
 342
 343 //    analyzeBridgesAndLaddersPatterns();
 344     analyzeTurnsAndHelicesPatterns();
 345 //    analyzePPHelicesPatterns();
 346     NoChainBreaksBetween(80, 75);
 347
 348 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 349 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 350 //    }
 351
 352 //    std::cout.precision(5);
 353 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 354 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 355 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 356 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 357 //        }
 358 //        else {
 359 //            std::cout << " has no donor[0] and" ;
 360 //        }
 361 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 362 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 363 //        }
 364 //        else {
 365 //            std::cout << " has no acceptor[0]" ;
 366 //        }
 367 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 368 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 369 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 370 //        }
 371 //        else {
 372 //            std::cout << " has no donor[1] and" ;
 373 //        }
 374 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 375 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 376 //        }
 377 //        else {
 378 //            std::cout << " has no acceptor[1]" ;
 379 //        }
 380 //    }
 381
 382     /*Write Data*/
 383
 384     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 385         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 386             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 387                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 388             }
 389         }
 390     }
 391
 392     /*Add breaks*/
 393
 394     if(SecondaryStructuresStatusMap.size() > 1){
 395         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 396             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 397                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 398                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 399                     ++linefactor;
 400                 }
 401             }
 402         }
 403     }
 404     return SecondaryStructuresStringLine;
 405 }
 406
 407 secondaryStructures::~secondaryStructures(){
 408     SecondaryStructuresStatusMap.resize(0);
 409     SecondaryStructuresStringLine.resize(0);
 410 }
 411
 412 DsspTool::DsspStorage::DsspStorage(){
 413     storaged_data.resize(0);
 414 }
 415
 416 void DsspTool::DsspStorage::clearAll(){
 417     storaged_data.resize(0);
 418 }
 419
 420 std::mutex DsspTool::DsspStorage::mx;
 421
 422 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 423     std::lock_guard<std::mutex> guardian(mx);
 424     std::pair<int, std::string> datapair(frnr, data);
 425     storaged_data.push_back(datapair);
 426 }
 427
 428 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 429     std::sort(storaged_data.begin(), storaged_data.end());
 430     return storaged_data;
 431 }
 432
 433 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 434     cutoff = cutoff_init;
 435 }
 436
 437 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 438     while (coordinate < 0) {
 439         coordinate += vector_length;
 440     }
 441     while (coordinate >= vector_length) {
 442         coordinate -= vector_length;
 443     }
 444 }
 445
 446 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 447     if (x < 0) {
 448         x += x_max;
 449     }
 450     if (x >= x_max) {
 451         x -= x_max;
 452     }
 453 }
 454
 455 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 456     rvec coordinates, box_vector_length;
 457     num_of_miniboxes.resize(0);
 458     num_of_miniboxes.resize(3);
 459     for (std::size_t i{XX}; i <= ZZ; ++i) {
 460         box_vector_length[i] = std::sqrt(
 461                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 462         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 463     }
 464     MiniBoxesMap.resize(0);
 465     MiniBoxesReverseMap.resize(0);
 466     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 467                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 468                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 469                              0))));
 470     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 471     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 472         for (std::size_t j{XX}; j <= ZZ; ++j) {
 473             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 474             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 475         }
 476         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 477                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 478         for (std::size_t j{XX}; j <= ZZ; ++j){
 479             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 480         }
 481     }
 482 }
 483
 484 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 485     GetMiniBoxesMap(fr, IndexMap);
 486     MiniBoxSize[XX] = MiniBoxesMap.size();
 487     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 488     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 489     PairMap.resize(0);
 490     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 491     ResiI = PairMap.begin();
 492     ResiJ = ResiI->begin();
 493
 494     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 495         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 496             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 497                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 498                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 499                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 500                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 501                     }
 502                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 503                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 504                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 505                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 506                         }
 507                     }
 508                 }
 509             }
 510         }
 511     }
 512 }
 513
 514 bool alternateNeighborhoodSearch::findNextPair(){
 515
 516     if(!PairMap.size()){
 517         return false;
 518     }
 519
 520     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 521         for(; ResiJ != ResiI->end(); ++ResiJ){
 522             if(*ResiJ){
 523                 resiIpos = ResiI - PairMap.begin();
 524                 resiJpos = ResiJ - ResiI->begin();
 525                 if ( ResiJ != ResiI->end() ){
 526                     ++ResiJ;
 527                 }
 528                 else if (ResiI != PairMap.end()) {
 529                     ++ResiI;
 530                     ResiJ = ResiI->begin();
 531                 }
 532                 else {
 533                     return false; // ???
 534                 }
 535                 return true;
 536             }
 537         }
 538     }
 539
 540     return false;
 541 }
 542
 543 std::size_t alternateNeighborhoodSearch::getResiI() const {
 544     return resiIpos;
 545 }
 546
 547 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 548     return resiJpos;
 549 }
 550
 551
 552 DsspTool::DsspStorage DsspTool::Storage;
 553
 554 DsspTool::DsspTool(){
 555 }
 556
 557 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 558 {
 559    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 560    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 561    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 562    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 563    {
 564        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 565                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 566                                     fr,
 567                                     pbc)
 568            > maxdist)
 569        {
 570            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 571            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 572
 573 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 574        }
 575    }
 576    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 577    {
 578        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 579            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 580            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 581            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 582           )
 583        {
 584            continue;
 585        }
 586        for (int j{ 0 }; j < 3; ++j)
 587        {
 588            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 589                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 590            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 591                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 592        }
 593        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 594        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 595                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 596                                         fr,
 597                                         pbc)
 598                * gmx::c_angstrom / gmx::c_nano
 599                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 600                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 601                                           fr,
 602                                           pbc)
 603                * gmx::c_angstrom / gmx::c_nano;
 604        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 605        if (degree > benddegree)
 606        {
 607            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 608        }
 609    }
 610 }
 611
 612 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 613                        ResInfo& Acceptor,
 614                        const t_trxframe&          fr,
 615                        const t_pbc*               pbc)
 616 {
 617    /*
 618     * DSSP uses eq from dssp 2.x
 619     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 620     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 621     * if R is in A
 622     * Hbond if E < -0.5
 623     */
 624
 625     const float kCouplingConstant = 27.888;
 626     const float minimalAtomDistance{ 0.5 },
 627             minEnergy{ -9.9 };
 628     float HbondEnergy{ 0 };
 629     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 630
 631    if( !(Donor.is_proline) ){
 632        if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 633            && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )  // Kinda ew
 634        {
 635
 636            distanceNO = CalculateAtomicDistances(
 637                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 638            distanceNC = CalculateAtomicDistances(
 639                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 640
 641            if (initParams.addHydrogens){
 642                if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 643 //                   std::cout << "On donor " << Donor.info->nr << *(Donor.info->name) << std::endl;
 644 //                   std::cout << "Prev donor is " << Donor.prevResi->info->nr << *(Donor.prevResi->info->name) << std::endl;
 645 //                   std::cout << "Prev C index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomC) << std::endl;
 646 //                   std::cout << "Prev O index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomO) << std::endl;
 647                    rvec atomH{};
 648                    float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 649                    for (int i{XX}; i <= ZZ; ++i){
 650                        float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 651                        atomH[i] = prevCO / prevCODist;
 652                    }
 653                    distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 654                    distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 655                }
 656                else{
 657                    distanceHO = distanceNO;
 658                    distanceHC = distanceNC;
 659                }
 660            }
 661            else {
 662                distanceHO = CalculateAtomicDistances(
 663                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 664                distanceHC = CalculateAtomicDistances(
 665                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 666            }
 667
 668            if (CalculateAtomicDistances(
 669                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 670                < minimalCAdistance)
 671            {
 672                if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 673                    || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 674                {
 675                    HbondEnergy = minEnergy;
 676
 677 //                   std::cout << "HBOND exists cause of distance" << std::endl;
 678                }
 679                else
 680                {
 681                    HbondEnergy =
 682                            kCouplingConstant
 683                            * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 684                    HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 685
 686 //                   std::cout.precision(5);
 687 //                   std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
 688
 689 //                   if ( HbondEnergy == 0){
 690 //                       std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
 691 //                   }
 692
 693                    if ( HbondEnergy < minEnergy ){
 694                        HbondEnergy = minEnergy;
 695                    }
 696                }
 697            }
 698        }
 699    }
 700 //   else {
 701 //       std::cerr << "PRO DETECTED! THIS IS RESI № " << Donor.info->nr << std::endl; //IT WORKS JUST FINE
 702 //   }
 703
 704    if (HbondEnergy < Donor.acceptorEnergy[0]){
 705        Donor.acceptor[1] = Donor.acceptor[0];
 706        Donor.acceptor[0] = Acceptor.info;
 707        Donor.acceptorEnergy[0] = HbondEnergy;
 708    }
 709    else if (HbondEnergy < Donor.acceptorEnergy[1]){
 710        Donor.acceptor[1] = Acceptor.info;
 711        Donor.acceptorEnergy[1] = HbondEnergy;
 712    }
 713
 714    if (HbondEnergy < Acceptor.donorEnergy[0]){
 715        Acceptor.donor[1] = Acceptor.donor[0];
 716        Acceptor.donor[0] = Donor.info;
 717        Acceptor.donorEnergy[0] = HbondEnergy;
 718    }
 719    else if (HbondEnergy < Acceptor.donorEnergy[1]){
 720        Acceptor.donor[1] = Donor.info;
 721        Acceptor.donorEnergy[1] = HbondEnergy;
 722    }
 723 }
 724
 725
 726 /* Calculate Distance From B to A */
 727 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 728 {
 729    gmx::RVec r{ 0, 0, 0 };
 730    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 731 //   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
 732    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 733 }
 734
 735 /* Calculate Distance From B to A, where A is only fake coordinates */
 736 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 737 {
 738    gmx::RVec r{ 0, 0, 0 };
 739    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 740 //   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
 741    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 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        }
 791        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 792        {
 793            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 794        }
 795
 796 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 797 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 798 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 799 //       }
 800    }
 801
 802    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 803        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 804
 805        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 806
 807 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 808 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 809 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 810 //         std::cout << IndexMap[j].prevResi->info->nr;
 811 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 812 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 813 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 814 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 815 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 816 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 817    }
 818
 819    nres = i + 1;
 820 }
 821
 822 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 823 {
 824
 825     switch(initParams.NBS){
 826     case (NBSearchMethod::Classique): {
 827
 828         // store positions of CA atoms to use them for nbSearch
 829         std::vector<gmx::RVec> positionsCA_;
 830         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 831         {
 832             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 833         }
 834
 835         AnalysisNeighborhood nb_;
 836         nb_.setCutoff(initParams.cutoff_);
 837         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 838         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 839         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 840         gmx::AnalysisNeighborhoodPair       pair;
 841         while (pairSearch.findNextPair(&pair))
 842         {
 843             if(CalculateAtomicDistances(
 844                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 845                 < minimalCAdistance){
 846                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 847                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 848                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 849                 }
 850             }
 851         }
 852
 853         break;
 854     }
 855     case (NBSearchMethod::Experimental): { // TODO FIX
 856
 857         alternateNeighborhoodSearch as_;
 858
 859         as_.setCutoff(initParams.cutoff_);
 860
 861         as_.AltPairSearch(fr, IndexMap);
 862
 863         while (as_.findNextPair()){
 864             if(CalculateAtomicDistances(
 865                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 866                 < minimalCAdistance){
 867                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 868                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 869                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 870                 }
 871             }
 872         }
 873
 874         break;
 875     }
 876     default: {
 877
 878         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 879             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 880                 if(CalculateAtomicDistances(
 881                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 882                     < minimalCAdistance){
 883                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 884                     if (Acceptor != Donor + 1){
 885                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 886                     }
 887                 }
 888             };
 889         };
 890         break;
 891     }
 892     }
 893
 894
 895 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 896 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 897 //    }
 898
 899    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 900    calculateBends(fr, pbc);
 901    Storage.storageData(frnr, PatternSearch.patternSearch());
 902
 903 }
 904
 905 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 906     return Storage.returnData();
 907 }
 908
 909 } // namespace analysismodules
 910
 911 } // namespace gmx