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,
  15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17 * Lesser General Public License for more details.
  18 *
  19 * You should have received a copy of the GNU Lesser General Public
  20 * License along with GROMACS; if not, see
  21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23 *
  24 * If you want to redistribute modifications to GROMACS, please
  25 * consider that scientific software is very special. Version
  26 * control is crucial - bugs must be traceable. We will be happy to
  27 * consider code for inclusion in the official distribution, but
  28 * derived work must not be called official GROMACS. Details are found
  29 * in the README & COPYING files - if they are missing, get the
  30 * official version at http://www.gromacs.org.
  31 *
  32 * To help us fund GROMACS development, we humbly ask that you cite
  33 * the research papers on the package. Check out http://www.gromacs.org.
  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     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 149     if ( i > j ){
 150         std::swap(i, j);
 151     }
 152
 153     for (; i != j; ++i){
 154         if ( !(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i])) ){
 155
 156         }
 157         std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 158         return false;
 159     }
 160     return true;
 161 }
 162
 163 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 164     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){
 165         return bridgeTypes::None;
 166     }
 167     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1)){
 168         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){ //possibly swap
 169             return bridgeTypes::ParallelBridge;
 170         }
 171         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){ //possibly swap
 172             return bridgeTypes::AntiParallelBridge;
 173         }
 174     }
 175     return bridgeTypes::None;
 176 }
 177
 178 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 179     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 180         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 181             bridgeTypes type {calculateBridge(i, j)};
 182             if (type == bridgeTypes::None){
 183                 continue;
 184             }
 185             bool found {false};
 186         }
 187     }
 188
 189
 190
 191
 192
 193
 194
 195
 196
 197
 198
 199
 200 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 201 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 202 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 203 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 204 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 205 //                    Bridge[i].push_back(j);
 206 //                }
 207 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 208 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 209 //                    AntiBridge[i].push_back(j);
 210 //                }
 211 //            }
 212 //        }
 213 //    }
 214 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 215 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 216 //            setStatus(i, secondaryStructureTypes::Bulge);
 217 //        }
 218 //    }
 219 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 220 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 221 //            if (j == i){
 222 //                continue;
 223 //            }
 224 //            else {
 225 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 226 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 227 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 228 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 229 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 230 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 231 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 232 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 233 //                                        < 5)){
 234 //                                    if (j < i){
 235 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 236 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 237 //                                        }
 238 //                                    }
 239 //                                    else{
 240 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 241 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 242 //                                        }
 243 //                                    }
 244 //                                }
 245 //                            }
 246 //                        }
 247 //                    }
 248 //                }
 249 //            }
 250 //        }
 251 //    }
 252 }
 253
 254 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 255     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 256         std::cout << "Testing Helix_" << static_cast<std::size_t>(i) + 3 << std::endl;
 257         std::size_t stride {static_cast<std::size_t>(i) + 3};
 258         for(std::size_t j {0}; j + static_cast<std::size_t>(i) < SecondaryStructuresStatusMap.size(); ++j){
 259             std::cout << "Testing " << j << " and " << j + stride << std::endl;
 260             if ( hasHBondBetween(j, j + (static_cast<std::size_t>(i))) && NoChainBreaksBetween(j, j + stride) ){
 261                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 262                 SecondaryStructuresStatusMap[j + static_cast<std::size_t>(i)].setStatus(HelixPositions::End, i);
 263
 264                 for (std::size_t k {1}; k < (static_cast<std::size_t>(i)); ++k){
 265                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 266                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 267                     }
 268
 269                 }
 270
 271                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 272                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 273                 }
 274                 else {
 275                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 276                 }
 277             }
 278         }
 279     }
 280
 281     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 282         std::size_t stride {static_cast<std::size_t>(i) + 3};
 283         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 284             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 285                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 286                 bool empty = true;
 287                 secondaryStructureTypes Helix;
 288                 switch(i){
 289                 case turnsTypes::Turn_3:
 290                     for (std::size_t k {0}; empty && k < stride; ++k){
 291                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 292                     }
 293                     Helix = secondaryStructureTypes::Helix_3;
 294                     break;
 295                 case turnsTypes::Turn_5:
 296                     for (std::size_t k {0}; empty && k < stride; ++k){
 297                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5));
 298                     }
 299                     Helix = secondaryStructureTypes::Helix_4;
 300                     break;
 301                 default:
 302                     Helix = secondaryStructureTypes::Helix_4;
 303                     break;
 304                 }
 305                 std::cout << j << " is HELIX" << std::endl;
 306                 if ( empty ){
 307                     for(std::size_t k {0}; k < (static_cast<std::size_t>(i)); ++k ){
 308                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 309                     }
 310                 }
 311             }
 312         }
 313     }
 314
 315     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 316         if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Loop)){
 317             bool isTurn = false;
 318             for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 319                 std::size_t stride {static_cast<std::size_t>(i) + 3};
 320                 for(std::size_t k {1}; k < stride; ++k){
 321                     isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 322                 }
 323             }
 324
 325             if (isTurn){
 326                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 327             }
 328             else if (SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 329                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 330             }
 331         }
 332     }
 333
 334 }
 335
 336 void secondaryStructures::analyzePPHelicesPatterns(){}
 337
 338 std::string secondaryStructures::patternSearch(){
 339
 340
 341 //    analyzeBridgesAndLaddersPatterns();
 342     analyzeTurnsAndHelicesPatterns();
 343 //    analyzePPHelicesPatterns();
 344     NoChainBreaksBetween(80, 75);
 345
 346 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 347 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 348 //    }
 349
 350 //    std::cout.precision(5);
 351 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 352 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 353 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 354 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 355 //        }
 356 //        else {
 357 //            std::cout << " has no donor[0] and" ;
 358 //        }
 359 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 360 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 361 //        }
 362 //        else {
 363 //            std::cout << " has no acceptor[0]" ;
 364 //        }
 365 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 366 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 367 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 368 //        }
 369 //        else {
 370 //            std::cout << " has no donor[1] and" ;
 371 //        }
 372 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 373 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 374 //        }
 375 //        else {
 376 //            std::cout << " has no acceptor[1]" ;
 377 //        }
 378 //    }
 379
 380     /*Write Data*/
 381
 382     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 383         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 384             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 385                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 386             }
 387         }
 388     }
 389
 390     /*Add breaks*/
 391
 392     if(SecondaryStructuresStatusMap.size() > 1){
 393         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 394             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 395                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 396                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 397                     ++linefactor;
 398                 }
 399             }
 400         }
 401     }
 402     return SecondaryStructuresStringLine;
 403 }
 404
 405 secondaryStructures::~secondaryStructures(){
 406     SecondaryStructuresStatusMap.resize(0);
 407     SecondaryStructuresStringLine.resize(0);
 408 }
 409
 410 DsspTool::DsspStorage::DsspStorage(){
 411     storaged_data.resize(0);
 412 }
 413
 414 void DsspTool::DsspStorage::clearAll(){
 415     storaged_data.resize(0);
 416 }
 417
 418 std::mutex DsspTool::DsspStorage::mx;
 419
 420 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 421     std::lock_guard<std::mutex> guardian(mx);
 422     std::pair<int, std::string> datapair(frnr, data);
 423     storaged_data.push_back(datapair);
 424 }
 425
 426 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 427     std::sort(storaged_data.begin(), storaged_data.end());
 428     return storaged_data;
 429 }
 430
 431 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 432     cutoff = cutoff_init;
 433 }
 434
 435 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 436     while (coordinate < 0) {
 437         coordinate += vector_length;
 438     }
 439     while (coordinate >= vector_length) {
 440         coordinate -= vector_length;
 441     }
 442 }
 443
 444 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 445     if (x < 0) {
 446         x += x_max;
 447     }
 448     if (x >= x_max) {
 449         x -= x_max;
 450     }
 451 }
 452
 453 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 454     rvec coordinates, box_vector_length;
 455     num_of_miniboxes.resize(0);
 456     num_of_miniboxes.resize(3);
 457     for (std::size_t i{XX}; i <= ZZ; ++i) {
 458         box_vector_length[i] = std::sqrt(
 459                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 460         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 461     }
 462     MiniBoxesMap.resize(0);
 463     MiniBoxesReverseMap.resize(0);
 464     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 465                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 466                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 467                              0))));
 468     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 469     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 470         for (std::size_t j{XX}; j <= ZZ; ++j) {
 471             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 472             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 473         }
 474         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 475                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 476         for (std::size_t j{XX}; j <= ZZ; ++j){
 477             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 478         }
 479     }
 480 }
 481
 482 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 483     GetMiniBoxesMap(fr, IndexMap);
 484     MiniBoxSize[XX] = MiniBoxesMap.size();
 485     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 486     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 487     PairMap.resize(0);
 488     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 489     ResiI = PairMap.begin();
 490     ResiJ = ResiI->begin();
 491
 492     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 493         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 494             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 495                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 496                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 497                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 498                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 499                     }
 500                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 501                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 502                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 503                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 504                         }
 505                     }
 506                 }
 507             }
 508         }
 509     }
 510 }
 511
 512 bool alternateNeighborhoodSearch::findNextPair(){
 513
 514     if(!PairMap.size()){
 515         return false;
 516     }
 517
 518     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 519         for(; ResiJ != ResiI->end(); ++ResiJ){
 520             if(*ResiJ){
 521                 resiIpos = ResiI - PairMap.begin();
 522                 resiJpos = ResiJ - ResiI->begin();
 523                 if ( ResiJ != ResiI->end() ){
 524                     ++ResiJ;
 525                 }
 526                 else if (ResiI != PairMap.end()) {
 527                     ++ResiI;
 528                     ResiJ = ResiI->begin();
 529                 }
 530                 else {
 531                     return false; // ???
 532                 }
 533                 return true;
 534             }
 535         }
 536     }
 537
 538     return false;
 539 }
 540
 541 std::size_t alternateNeighborhoodSearch::getResiI() const {
 542     return resiIpos;
 543 }
 544
 545 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 546     return resiJpos;
 547 }
 548
 549
 550 DsspTool::DsspStorage DsspTool::Storage;
 551
 552 DsspTool::DsspTool(){
 553 }
 554
 555 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 556 {
 557    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 558    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 559    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 560    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 561    {
 562        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 563                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 564                                     fr,
 565                                     pbc)
 566            > maxdist)
 567        {
 568            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 569            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 570
 571 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 572        }
 573    }
 574    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 575    {
 576        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 577            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 578            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 579            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 580           )
 581        {
 582            continue;
 583        }
 584        for (int j{ 0 }; j < 3; ++j)
 585        {
 586            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 587                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 588            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 589                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 590        }
 591        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 592        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 593                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 594                                         fr,
 595                                         pbc)
 596                * gmx::c_angstrom / gmx::c_nano
 597                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 598                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 599                                           fr,
 600                                           pbc)
 601                * gmx::c_angstrom / gmx::c_nano;
 602        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 603        if (degree > benddegree)
 604        {
 605            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 606        }
 607    }
 608 }
 609
 610 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 611                        ResInfo& Acceptor,
 612                        const t_trxframe&          fr,
 613                        const t_pbc*               pbc)
 614 {
 615    /*
 616     * DSSP uses eq from dssp 2.x
 617     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 618     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 619     * if R is in A
 620     * Hbond if E < -0.5
 621     */
 622
 623     const float kCouplingConstant = 27.888;
 624     const float minimalAtomDistance{ 0.5 },
 625             minEnergy{ -9.9 };
 626     float HbondEnergy{ 0 };
 627     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 628
 629    if( !(Donor.is_proline) ){
 630        if (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 631            && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || (initParams.addHydrogens) ) )  // Kinda ew
 632        {
 633
 634            distanceNO = CalculateAtomicDistances(
 635                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 636            distanceNC = CalculateAtomicDistances(
 637                    Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 638
 639            if (initParams.addHydrogens){
 640                if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 641 //                   std::cout << "On donor " << Donor.info->nr << *(Donor.info->name) << std::endl;
 642 //                   std::cout << "Prev donor is " << Donor.prevResi->info->nr << *(Donor.prevResi->info->name) << std::endl;
 643 //                   std::cout << "Prev C index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomC) << std::endl;
 644 //                   std::cout << "Prev O index is " << Donor.prevResi->getIndex(backboneAtomTypes::AtomO) << std::endl;
 645                    rvec atomH{};
 646                    float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 647                    for (int i{XX}; i <= ZZ; ++i){
 648                        float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 649                        atomH[i] = prevCO / prevCODist;
 650                    }
 651                    distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 652                    distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 653                }
 654                else{
 655                    distanceHO = distanceNO;
 656                    distanceHC = distanceNC;
 657                }
 658            }
 659            else {
 660                distanceHO = CalculateAtomicDistances(
 661                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 662                distanceHC = CalculateAtomicDistances(
 663                        Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 664            }
 665
 666            if (CalculateAtomicDistances(
 667                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 668                < minimalCAdistance)
 669            {
 670                if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 671                    || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 672                {
 673                    HbondEnergy = minEnergy;
 674
 675 //                   std::cout << "HBOND exists cause of distance" << std::endl;
 676                }
 677                else
 678                {
 679                    HbondEnergy =
 680                            kCouplingConstant
 681                            * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 682                    HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 683
 684 //                   std::cout.precision(5);
 685 //                   std::cout << "Calculated ENERGY = " << HbondEnergy << std::endl;
 686
 687 //                   if ( HbondEnergy == 0){
 688 //                       std::cout << "Calculated ENERGY = " << HbondEnergy << " For donor " << Donor.info->nr << " and acceptor " << Acceptor.info->nr << std::endl;
 689 //                   }
 690
 691                    if ( HbondEnergy < minEnergy ){
 692                        HbondEnergy = minEnergy;
 693                    }
 694                }
 695            }
 696        }
 697    }
 698 //   else {
 699 //       std::cerr << "PRO DETECTED! THIS IS RESI № " << Donor.info->nr << std::endl; //IT WORKS JUST FINE
 700 //   }
 701
 702    if (HbondEnergy < Donor.acceptorEnergy[0]){
 703        Donor.acceptor[1] = Donor.acceptor[0];
 704        Donor.acceptor[0] = Acceptor.info;
 705        Donor.acceptorEnergy[0] = HbondEnergy;
 706    }
 707    else if (HbondEnergy < Donor.acceptorEnergy[1]){
 708        Donor.acceptor[1] = Acceptor.info;
 709        Donor.acceptorEnergy[1] = HbondEnergy;
 710    }
 711
 712    if (HbondEnergy < Acceptor.donorEnergy[0]){
 713        Acceptor.donor[1] = Acceptor.donor[0];
 714        Acceptor.donor[0] = Donor.info;
 715        Acceptor.donorEnergy[0] = HbondEnergy;
 716    }
 717    else if (HbondEnergy < Acceptor.donorEnergy[1]){
 718        Acceptor.donor[1] = Donor.info;
 719        Acceptor.donorEnergy[1] = HbondEnergy;
 720    }
 721 }
 722
 723
 724 /* Calculate Distance From B to A */
 725 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 726 {
 727    gmx::RVec r{ 0, 0, 0 };
 728    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 729 //   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
 730    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 731 }
 732
 733 /* Calculate Distance From B to A, where A is only fake coordinates */
 734 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 735 {
 736    gmx::RVec r{ 0, 0, 0 };
 737    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 738 //   return r.norm(); // TODO * gmx::c_nm2A; if not PDB, i guess????
 739    return r.norm() * gmx::c_nm2A; // TODO * gmx::c_nm2A; if not PDB, i guess????
 740 }
 741
 742 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 743 {
 744
 745    std::cout << "Init started" << std::endl;
 746    initParams = initParamz;
 747    ResInfo _backboneAtoms;
 748    std::size_t                 i{ 0 };
 749    std::string proLINE;
 750    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
 751    IndexMap.resize(0);
 752    IndexMap.push_back(_backboneAtoms);
 753    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 754    proLINE = *(IndexMap[i].info->name);
 755    if( proLINE.compare("PRO") == 0 ){
 756        IndexMap[i].is_proline = true;
 757    }
 758
 759    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
 760        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
 761        {
 762            ++i;
 763            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
 764            IndexMap.emplace_back(_backboneAtoms);
 765            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 766            proLINE = *(IndexMap[i].info->name);
 767            if( proLINE.compare("PRO") == 0 ){
 768                IndexMap[i].is_proline = true;
 769            }
 770
 771        }
 772        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
 773        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
 774        {
 775            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
 776        }
 777        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
 778        {
 779            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
 780        }
 781        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
 782        {
 783            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
 784        }
 785        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
 786        {
 787            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
 788        }
 789        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 790        {
 791            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 792        }
 793
 794 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 795 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 796 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 797 //       }
 798    }
 799
 800    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 801        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 802
 803        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 804
 805 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 806 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 807 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 808 //         std::cout << IndexMap[j].prevResi->info->nr;
 809 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 810 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 811 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 812 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 813 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 814 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 815    }
 816
 817    nres = i + 1;
 818 }
 819
 820 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 821 {
 822
 823     switch(initParams.NBS){
 824     case (NBSearchMethod::Classique): {
 825
 826         // store positions of CA atoms to use them for nbSearch
 827         std::vector<gmx::RVec> positionsCA_;
 828         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 829         {
 830             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 831         }
 832
 833         AnalysisNeighborhood nb_;
 834         nb_.setCutoff(initParams.cutoff_);
 835         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 836         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 837         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 838         gmx::AnalysisNeighborhoodPair       pair;
 839         while (pairSearch.findNextPair(&pair))
 840         {
 841             if(CalculateAtomicDistances(
 842                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 843                 < minimalCAdistance){
 844                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 845                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 846                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 847                 }
 848             }
 849         }
 850
 851         break;
 852     }
 853     case (NBSearchMethod::Experimental): { // TODO FIX
 854
 855         alternateNeighborhoodSearch as_;
 856
 857         as_.setCutoff(initParams.cutoff_);
 858
 859         as_.AltPairSearch(fr, IndexMap);
 860
 861         while (as_.findNextPair()){
 862             if(CalculateAtomicDistances(
 863                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 864                 < minimalCAdistance){
 865                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 866                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 867                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 868                 }
 869             }
 870         }
 871
 872         break;
 873     }
 874     default: {
 875
 876         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 877             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 878                 if(CalculateAtomicDistances(
 879                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 880                     < minimalCAdistance){
 881                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 882                     if (Acceptor != Donor + 1){
 883                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 884                     }
 885                 }
 886             };
 887         };
 888         break;
 889     }
 890     }
 891
 892
 893 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 894 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 895 //    }
 896
 897    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 898    calculateBends(fr, pbc);
 899    Storage.storageData(frnr, PatternSearch.patternSearch());
 900
 901 }
 902
 903 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 904     return Storage.returnData();
 905 }
 906
 907 } // namespace analysismodules
 908
 909 } // namespace gmx