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. Reason(s): " ;
 130 //        if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 131 //            std::cout << "Donor has no acceptor[0]; ";
 132 //        }
 133 //        if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 134 //            std::cout << "Donor has no acceptor[1]; ";
 135 //        }
 136 //        if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 137 //            std::cout << "No info about acceptor; ";
 138 //        }
 139 //        std::cout << std::endl;
 140         return false;
 141     }
 142 //    else {
 143
 144 //        std::cout << "Comparing DONOR " << Donor << " And ACCEPTOR " << Acceptor << ": ";
 145 //        std::cout << "DONOR's acceptor adresses are " << (*ResInfoMap)[Donor].acceptor[0] << ", " << (*ResInfoMap)[Donor].acceptor[1] << " and ACCEPTOR adress is " << (*ResInfoMap)[Acceptor].info << std::endl;
 146 //        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;
 147 //        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;
 148
 149 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 150 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 151 //            std::cout << "HBond Exist" << std::endl;
 152 //        }
 153
 154 //
 155
 156
 157 //    }
 158
 159     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 160            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 161
 162
 163 }
 164
 165 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 166     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 167     if ( i > j ){
 168         std::swap(i, j);
 169     }
 170
 171     for (; i != j; ++i){
 172         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 173             std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 174             return false;
 175         }
 176     }
 177     return true;
 178 }
 179
 180 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 181     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
 182         return bridgeTypes::None;
 183     }
 184     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
 185         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
 186             return bridgeTypes::ParallelBridge;
 187         }
 188         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
 189             return bridgeTypes::AntiParallelBridge;
 190         }
 191     }
 192     return bridgeTypes::None;
 193 }
 194
 195 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 196     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 197         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 198             bridgeTypes type {calculateBridge(i, j)};
 199             if (type == bridgeTypes::None){
 200                 continue;
 201             }
 202             bool found {false};
 203         }
 204     }
 205
 206
 207
 208
 209
 210
 211
 212
 213
 214
 215
 216
 217 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 218 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 219 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 220 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 221 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 222 //                    Bridge[i].push_back(j);
 223 //                }
 224 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 225 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 226 //                    AntiBridge[i].push_back(j);
 227 //                }
 228 //            }
 229 //        }
 230 //    }
 231 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 232 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 233 //            setStatus(i, secondaryStructureTypes::Bulge);
 234 //        }
 235 //    }
 236 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 237 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 238 //            if (j == i){
 239 //                continue;
 240 //            }
 241 //            else {
 242 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 243 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 244 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 245 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 246 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 247 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 248 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 249 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 250 //                                        < 5)){
 251 //                                    if (j < i){
 252 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 253 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 254 //                                        }
 255 //                                    }
 256 //                                    else{
 257 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 258 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 259 //                                        }
 260 //                                    }
 261 //                                }
 262 //                            }
 263 //                        }
 264 //                    }
 265 //                }
 266 //            }
 267 //        }
 268 //    }
 269 }
 270
 271 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 272     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 273         std::size_t stride {static_cast<std::size_t>(i) + 3};
 274         std::cout << "Testing Helix_" << stride << std::endl;
 275         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 276 //            std::cout << "Testing " << j << " and " << j + stride << std::endl;
 277             if ( hasHBondBetween(j, j + stride) && NoChainBreaksBetween(j, j + stride) ){
 278                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 279                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 280
 281                 for (std::size_t k {1}; k < stride; ++k){
 282                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 283                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 284                         SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 285                     }
 286
 287                 }
 288
 289                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 290                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 291                 }
 292                 else {
 293                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 294                 }
 295             }
 296         }
 297     }
 298
 299     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 300         std::size_t stride {static_cast<std::size_t>(i) + 3};
 301         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 302             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 303                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 304                 bool empty = true;
 305                 secondaryStructureTypes Helix;
 306                 switch(i){
 307                 case turnsTypes::Turn_3:
 308                     for (std::size_t k {0}; empty && k < stride; ++k){
 309                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 310                     }
 311                     Helix = secondaryStructureTypes::Helix_3;
 312                     break;
 313                 case turnsTypes::Turn_5:
 314                     for (std::size_t k {0}; empty && k < stride; ++k){
 315                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 316                     }
 317                     Helix = secondaryStructureTypes::Helix_5;
 318                     break;
 319                 default:
 320                     Helix = secondaryStructureTypes::Helix_4;
 321                     break;
 322                 }
 323                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 324                     for(std::size_t k {0}; k < stride - 1; ++k ){
 325                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 326                     }
 327                 }
 328             }
 329         }
 330     }
 331
 332 //    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 333 //        if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
 334 //            bool isTurn = false;
 335 //            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 336 //                std::size_t stride {static_cast<std::size_t>(i) + 3};
 337 //                for(std::size_t k {1}; k < stride; ++k){
 338 //                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 339 //                }
 340 //            }
 341
 342 //            if (isTurn){
 343 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 344 //            }
 345 //            else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 346 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 347 //            }
 348 //        }
 349 //    }
 350
 351 }
 352
 353 void secondaryStructures::analyzePPHelicesPatterns(){}
 354
 355 std::string secondaryStructures::patternSearch(){
 356
 357
 358 //    analyzeBridgesAndLaddersPatterns();
 359     analyzeTurnsAndHelicesPatterns();
 360 //    analyzePPHelicesPatterns();
 361
 362 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 363 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 364 //    }
 365
 366 //    std::cout.precision(5);
 367 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 368 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 369 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 370 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 371 //        }
 372 //        else {
 373 //            std::cout << " has no donor[0] and" ;
 374 //        }
 375 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 376 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 377 //        }
 378 //        else {
 379 //            std::cout << " has no acceptor[0]" ;
 380 //        }
 381 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 382 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 383 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 384 //        }
 385 //        else {
 386 //            std::cout << " has no donor[1] and" ;
 387 //        }
 388 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 389 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 390 //        }
 391 //        else {
 392 //            std::cout << " has no acceptor[1]" ;
 393 //        }
 394 //    }
 395
 396     /*Write Data*/
 397
 398     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 399         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 400             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 401                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 402             }
 403         }
 404     }
 405
 406     /*Add breaks*/
 407
 408     if(SecondaryStructuresStatusMap.size() > 1){
 409         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 410             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 411                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 412                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 413                     ++linefactor;
 414                 }
 415             }
 416         }
 417     }
 418     return SecondaryStructuresStringLine;
 419 }
 420
 421 secondaryStructures::~secondaryStructures(){
 422     SecondaryStructuresStatusMap.resize(0);
 423     SecondaryStructuresStringLine.resize(0);
 424 }
 425
 426 DsspTool::DsspStorage::DsspStorage(){
 427     storaged_data.resize(0);
 428 }
 429
 430 void DsspTool::DsspStorage::clearAll(){
 431     storaged_data.resize(0);
 432 }
 433
 434 std::mutex DsspTool::DsspStorage::mx;
 435
 436 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 437     std::lock_guard<std::mutex> guardian(mx);
 438     std::pair<int, std::string> datapair(frnr, data);
 439     storaged_data.push_back(datapair);
 440 }
 441
 442 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 443     std::sort(storaged_data.begin(), storaged_data.end());
 444     return storaged_data;
 445 }
 446
 447 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 448     cutoff = cutoff_init;
 449 }
 450
 451 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 452     while (coordinate < 0) {
 453         coordinate += vector_length;
 454     }
 455     while (coordinate >= vector_length) {
 456         coordinate -= vector_length;
 457     }
 458 }
 459
 460 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 461     if (x < 0) {
 462         x += x_max;
 463     }
 464     if (x >= x_max) {
 465         x -= x_max;
 466     }
 467 }
 468
 469 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 470     rvec coordinates, box_vector_length;
 471     num_of_miniboxes.resize(0);
 472     num_of_miniboxes.resize(3);
 473     for (std::size_t i{XX}; i <= ZZ; ++i) {
 474         box_vector_length[i] = std::sqrt(
 475                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 476         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 477     }
 478     MiniBoxesMap.resize(0);
 479     MiniBoxesReverseMap.resize(0);
 480     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 481                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 482                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 483                              0))));
 484     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 485     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 486         for (std::size_t j{XX}; j <= ZZ; ++j) {
 487             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 488             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 489         }
 490         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 491                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 492         for (std::size_t j{XX}; j <= ZZ; ++j){
 493             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 494         }
 495     }
 496 }
 497
 498 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 499     GetMiniBoxesMap(fr, IndexMap);
 500     MiniBoxSize[XX] = MiniBoxesMap.size();
 501     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 502     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 503     PairMap.resize(0);
 504     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 505     ResiI = PairMap.begin();
 506     ResiJ = ResiI->begin();
 507
 508     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 509         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 510             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 511                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 512                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 513                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 514                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 515                     }
 516                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 517                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 518                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 519                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 520                         }
 521                     }
 522                 }
 523             }
 524         }
 525     }
 526 }
 527
 528 bool alternateNeighborhoodSearch::findNextPair(){
 529
 530     if(!PairMap.size()){
 531         return false;
 532     }
 533
 534     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 535         for(; ResiJ != ResiI->end(); ++ResiJ){
 536             if(*ResiJ){
 537                 resiIpos = ResiI - PairMap.begin();
 538                 resiJpos = ResiJ - ResiI->begin();
 539                 if ( ResiJ != ResiI->end() ){
 540                     ++ResiJ;
 541                 }
 542                 else if (ResiI != PairMap.end()) {
 543                     ++ResiI;
 544                     ResiJ = ResiI->begin();
 545                 }
 546                 else {
 547                     return false; // ???
 548                 }
 549                 return true;
 550             }
 551         }
 552     }
 553
 554     return false;
 555 }
 556
 557 std::size_t alternateNeighborhoodSearch::getResiI() const {
 558     return resiIpos;
 559 }
 560
 561 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 562     return resiJpos;
 563 }
 564
 565
 566 DsspTool::DsspStorage DsspTool::Storage;
 567
 568 DsspTool::DsspTool(){
 569 }
 570
 571 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 572 {
 573    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 574    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 575    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 576    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 577    {
 578        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 579                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 580                                     fr,
 581                                     pbc)
 582            > maxdist)
 583        {
 584            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 585            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 586
 587 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 588        }
 589    }
 590    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 591    {
 592        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 593            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 594            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 595            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 596           )
 597        {
 598            continue;
 599        }
 600        for (int j{ 0 }; j < 3; ++j)
 601        {
 602            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 603                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 604            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 605                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 606        }
 607        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 608        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 609                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 610                                         fr,
 611                                         pbc)
 612                * gmx::c_angstrom / gmx::c_nano
 613                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 614                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 615                                           fr,
 616                                           pbc)
 617                * gmx::c_angstrom / gmx::c_nano;
 618        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 619        if (degree > benddegree)
 620        {
 621            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 622        }
 623    }
 624 }
 625
 626 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 627                        ResInfo& Acceptor,
 628                        const t_trxframe&          fr,
 629                        const t_pbc*               pbc)
 630 {
 631    /*
 632     * DSSP uses eq from dssp 2.x
 633     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 634     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 635     * if R is in A
 636     * Hbond if E < -0.5
 637     *
 638     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 639     *
 640     */
 641
 642     const float kCouplingConstant = 27.888;
 643     const float minimalAtomDistance{ 0.5 },
 644             minEnergy{ -9.9 };
 645     float HbondEnergy{ 0 };
 646     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 647
 648     std::cout << "For Donor №" << Donor.info->nr - 1 << " and accpetor №" << Acceptor.info->nr - 1 << std::endl;
 649
 650    if( !(Donor.is_proline) ){
 651        if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 652            && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )
 653        {
 654
 655            distanceNO = CalculateAtomicDistances(
 656                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 657            distanceNC = CalculateAtomicDistances(
 658                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 659
 660            if (initParams.addHydrogens){
 661                if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 662                    rvec atomH{};
 663                    float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 664                    for (int i{XX}; i <= ZZ; ++i){
 665                        float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 666                        atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 667                        atomH[i] += prevCO / prevCODist;
 668                    }
 669                    distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 670                    distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 671                }
 672                else{
 673                    distanceHO = distanceNO;
 674                    distanceHC = distanceNC;
 675                }
 676            }
 677            else {
 678                distanceHO = CalculateAtomicDistances(
 679                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 680                distanceHC = CalculateAtomicDistances(
 681                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 682            }
 683
 684            if (CalculateAtomicDistances(
 685                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 686                < minimalCAdistance)
 687            {
 688                if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 689                    || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 690                {
 691                    HbondEnergy = minEnergy;
 692                }
 693                else
 694                {
 695                    HbondEnergy =
 696                            kCouplingConstant
 697                            * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 698 //                   HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 699
 700 //                   std::cout.precision(5);
 701 //                   std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
 702
 703 //                   if ( HbondEnergy == 0){
 704 //                       std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
 705 //                   }
 706
 707                    if ( HbondEnergy < minEnergy ){
 708                        HbondEnergy = minEnergy;
 709                    }
 710                }
 711            }
 712        }
 713
 714
 715
 716        std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 717                         Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 718        std::cout << "N-O distance: " << distanceNO << std::endl;
 719        std::cout << "N-C distance: " << distanceNC << std::endl;
 720        std::cout << "H-O distance: " << distanceHO << std::endl;
 721        std::cout << "H-C distance: " << distanceHC << std::endl;
 722
 723    }
 724
 725
 726    std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 727
 728
 729    if (HbondEnergy < Donor.acceptorEnergy[0]){
 730        Donor.acceptor[1] = Donor.acceptor[0];
 731        Donor.acceptor[0] = Acceptor.info;
 732        Donor.acceptorEnergy[0] = HbondEnergy;
 733    }
 734    else if (HbondEnergy < Donor.acceptorEnergy[1]){
 735        Donor.acceptor[1] = Acceptor.info;
 736        Donor.acceptorEnergy[1] = HbondEnergy;
 737    }
 738
 739    if (HbondEnergy < Acceptor.donorEnergy[0]){
 740        Acceptor.donor[1] = Acceptor.donor[0];
 741        Acceptor.donor[0] = Donor.info;
 742        Acceptor.donorEnergy[0] = HbondEnergy;
 743    }
 744    else if (HbondEnergy < Acceptor.donorEnergy[1]){
 745        Acceptor.donor[1] = Donor.info;
 746        Acceptor.donorEnergy[1] = HbondEnergy;
 747    }
 748 }
 749
 750
 751 /* Calculate Distance From B to A */
 752 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 753 {
 754    gmx::RVec r{ 0, 0, 0 };
 755    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 756    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 757 }
 758
 759 /* Calculate Distance From B to A, where A is only fake coordinates */
 760 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 761 {
 762    gmx::RVec r{ 0, 0, 0 };
 763    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 764    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 765 }
 766
 767 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 768 {
 769
 770    std::cout << "Init started" << std::endl;
 771    initParams = initParamz;
 772    ResInfo _backboneAtoms;
 773    std::size_t                 i{ 0 };
 774    std::string proLINE;
 775    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
 776    IndexMap.resize(0);
 777    IndexMap.push_back(_backboneAtoms);
 778    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 779    proLINE = *(IndexMap[i].info->name);
 780    if( proLINE.compare("PRO") == 0 ){
 781        IndexMap[i].is_proline = true;
 782    }
 783
 784    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
 785        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
 786        {
 787            ++i;
 788            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
 789            IndexMap.emplace_back(_backboneAtoms);
 790            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 791            proLINE = *(IndexMap[i].info->name);
 792            if( proLINE.compare("PRO") == 0 ){
 793                IndexMap[i].is_proline = true;
 794            }
 795
 796        }
 797        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
 798        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
 799        {
 800            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
 801        }
 802        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
 803        {
 804            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
 805        }
 806        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
 807        {
 808            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
 809        }
 810        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
 811        {
 812            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
 813            if (initParamz.addHydrogens == true){
 814                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 815            }
 816        }
 817        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 818        {
 819            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 820        }
 821
 822
 823
 824 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 825 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 826 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 827 //       }
 828    }
 829
 830    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 831        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 832
 833        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 834
 835 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 836 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 837 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 838 //         std::cout << IndexMap[j].prevResi->info->nr;
 839 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 840 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 841 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 842 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 843 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 844 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 845    }
 846
 847    nres = i + 1;
 848 }
 849
 850 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 851 {
 852
 853     switch(initParams.NBS){
 854     case (NBSearchMethod::Classique): {
 855
 856         // store positions of CA atoms to use them for nbSearch
 857         std::vector<gmx::RVec> positionsCA_;
 858         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 859         {
 860             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 861         }
 862
 863         AnalysisNeighborhood nb_;
 864         nb_.setCutoff(initParams.cutoff_);
 865         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 866         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 867         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 868         gmx::AnalysisNeighborhoodPair       pair;
 869         while (pairSearch.findNextPair(&pair))
 870         {
 871             if(CalculateAtomicDistances(
 872                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 873                 < minimalCAdistance){
 874                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 875                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 876                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 877                 }
 878             }
 879         }
 880
 881         break;
 882     }
 883     case (NBSearchMethod::Experimental): { // TODO FIX
 884
 885         alternateNeighborhoodSearch as_;
 886
 887         as_.setCutoff(initParams.cutoff_);
 888
 889         as_.AltPairSearch(fr, IndexMap);
 890
 891         while (as_.findNextPair()){
 892             if(CalculateAtomicDistances(
 893                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 894                 < minimalCAdistance){
 895                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 896                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 897                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 898                 }
 899             }
 900         }
 901
 902         break;
 903     }
 904     default: {
 905
 906         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 907             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 908                 if(CalculateAtomicDistances(
 909                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 910                     < minimalCAdistance){
 911                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 912                     if (Acceptor != Donor + 1){
 913                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 914                     }
 915                 }
 916             }
 917         }
 918         break;
 919     }
 920     }
 921
 922
 923 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 924 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 925 //    }
 926
 927    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 928    calculateBends(fr, pbc);
 929    Storage.storageData(frnr, PatternSearch.patternSearch());
 930
 931 }
 932
 933 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 934     return Storage.returnData();
 935 }
 936
 937 } // namespace analysismodules
 938
 939 } // namespace gmx