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 calculations of redidues with E ≈ -0
  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     SecondaryStructuresStatus = secondaryStructureTypeName;
  98 }
  99
 100 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
 101     TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
 102 }
 103
 104 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
 105     return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
 106 }
 107
 108 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
 109     return breakPartners[0] == partner || breakPartners[1] == partner;
 110 }
 111
 112 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
 113     return TurnsStatusArray[static_cast<std::size_t>(turn)];
 114 }
 115
 116 secondaryStructureTypes secondaryStructures::secondaryStructuresData::getStatus() const{
 117     return  SecondaryStructuresStatus;
 118 }
 119
 120 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
 121     if (breakPartners[0] == nullptr){
 122         breakPartners[0] = breakPartner;
 123     }
 124     else{
 125         breakPartners[1] = breakPartner;
 126     }
 127     setStatus(secondaryStructureTypes::Break);
 128 }
 129
 130 void secondaryStructures::secondaryStructuresData::setBridge(secondaryStructuresData *bridgePartner, std::size_t bridgePartnerIndex, bridgeTypes bridgeType){
 131     if(bridgeType == bridgeTypes::ParallelBridge){
 132         bridgePartners[0] = bridgePartner;
 133         bridgePartnersIndexes[0] = bridgePartnerIndex;
 134     }
 135     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 136         bridgePartners[1] = bridgePartner;
 137         bridgePartnersIndexes[1] = bridgePartnerIndex;
 138     }
 139 }
 140
 141 bool secondaryStructures::secondaryStructuresData::hasBridges() const{
 142     return bridgePartners[0] || bridgePartners[1];
 143
 144 }
 145
 146 bool secondaryStructures::secondaryStructuresData::hasBridges(bridgeTypes bridgeType) const{
 147     if(bridgeType == bridgeTypes::ParallelBridge){
 148         return bridgePartners[0] != nullptr;
 149     }
 150     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 151         return bridgePartners[1] != nullptr;
 152     }
 153
 154     return false;
 155
 156 }
 157
 158 bool secondaryStructures::secondaryStructuresData::isBridgePartnerWith(secondaryStructuresData *bridgePartner, bridgeTypes bridgeType) const{
 159     if(bridgeType == bridgeTypes::ParallelBridge){
 160         return bridgePartners[0] == bridgePartner;
 161     }
 162     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 163         return bridgePartners[1] == bridgePartner;
 164     }
 165     return false;
 166 }
 167
 168 std::size_t secondaryStructures::secondaryStructuresData::getBridgePartnerIndex(bridgeTypes bridgeType) const{
 169     if (bridgeType == bridgeTypes::ParallelBridge){
 170         return bridgePartnersIndexes[0];
 171     }
 172     return bridgePartnersIndexes[1];
 173 }
 174
 175 secondaryStructures::secondaryStructuresData secondaryStructures::secondaryStructuresData::getBridgePartner(bridgeTypes bridgeType) const{
 176     if(bridgeType == bridgeTypes::ParallelBridge){
 177         return *(bridgePartners[0]);
 178     }
 179     return *(bridgePartners[1]);
 180 }
 181
 182 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
 183     if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
 184         (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
 185         (*ResInfoMap)[Acceptor].info == nullptr ){
 186 //        std::cout << "Bad hbond check. Reason(s): " ;
 187 //        if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 188 //            std::cout << "Donor has no acceptor[0]; ";
 189 //        }
 190 //        if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 191 //            std::cout << "Donor has no acceptor[1]; ";
 192 //        }
 193 //        if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 194 //            std::cout << "No info about acceptor; ";
 195 //        }
 196 //        std::cout << std::endl;
 197         return false;
 198     }
 199 //    else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
 200 //              (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
 201 //              (*ResInfoMap)[Donor].info == nullptr )) {
 202 //        std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
 203 //        std::cout << "Donor's acceptors' nr are = " << (*ResInfoMap)[Donor].acceptor[0]->nr << " (chain " << (*ResInfoMap)[Donor].acceptor[0]->chainid << ") , " << (*ResInfoMap)[Donor].acceptor[1]->nr << " (chain " << (*ResInfoMap)[Donor].acceptor[1]->chainid << ")" << std::endl;
 204 //        std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
 205 //        std::cout << "Acceptors's donors' nr are = " << (*ResInfoMap)[Acceptor].donor[0]->nr << " (chain " << (*ResInfoMap)[Acceptor].donor[0]->chainid << ") , " << (*ResInfoMap)[Acceptor].donor[1]->nr << " (chain " << (*ResInfoMap)[Acceptor].donor[1]->chainid << ")" << std::endl;
 206 //        std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
 207 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 208 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 209 //            std::cout << "HBond Exist" << std::endl;
 210 //        }
 211 //    }
 212 //    else {
 213 //        std::cout << "Bad hbond check. Reason(s): " ;
 214 //        if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
 215 //            std::cout << "Acceptor has no donor[0]; ";
 216 //        }
 217 //        if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
 218 //            std::cout << "Acceptor has no donor[1]; ";
 219 //        }
 220 //        if ( (*ResInfoMap)[Donor].info == nullptr ){
 221 //            std::cout << "No info about donor; ";
 222 //        }
 223 //        std::cout << std::endl;
 224 //    }
 225
 226     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 227            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 228
 229
 230 }
 231
 232 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 233     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 234     if ( i > j ){
 235         std::swap(i, j);
 236     }
 237
 238     for (; i != j; ++i){
 239         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 240 //            std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 241             return false;
 242         }
 243     }
 244     return true;
 245 }
 246
 247 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 248     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){ // Protection from idiotz, не обязательно нужен
 249         return bridgeTypes::None;
 250     }
 251
 252     ResInfo a{(*ResInfoMap)[i]}, b{(*ResInfoMap)[j]};
 253
 254     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1) && a.prevResi && a.nextResi && b.prevResi && b.nextResi){
 255         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){
 256             return bridgeTypes::ParallelBridge;
 257         }
 258         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){
 259             return bridgeTypes::AntiParallelBridge;
 260         }
 261     }
 262     return bridgeTypes::None;
 263 }
 264
 265 void secondaryStructures::analyzeBridgesAndStrandsPatterns(){
 266 //  Calculate Bridgez
 267     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 268         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 269             switch(calculateBridge(i, j)){
 270             case bridgeTypes::ParallelBridge : {
 271                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::ParallelBridge);
 272                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 273                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::ParallelBridge);
 274                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 275             }
 276             case bridgeTypes::AntiParallelBridge : {
 277                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::AntiParallelBridge);
 278                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 279                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::AntiParallelBridge);
 280                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 281             }
 282             default :
 283                 continue;
 284             }
 285         }
 286     }
 287 //  Calculate Extended Strandz
 288     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 289         bool is_Estrand {false};
 290         for(std::size_t j {2}; j != 0; --j){
 291             for(const bridgeTypes &bridgeType : {bridgeTypes::ParallelBridge, bridgeTypes::AntiParallelBridge}){
 292                 if (SecondaryStructuresStatusMap[i].hasBridges(bridgeType) && SecondaryStructuresStatusMap[i + j].hasBridges(bridgeType) ){
 293                     std::size_t i_partner{SecondaryStructuresStatusMap[i].getBridgePartnerIndex(bridgeType)}, j_partner{SecondaryStructuresStatusMap[i + j].getBridgePartnerIndex(bridgeType)}, second_strand{};
 294 //                    std::cout << "i = " << i << std::endl;
 295 //                    std::cout << "j = " << j << std::endl;
 296 //                    std::cout << "i_partner = " << i_partner << std::endl;
 297 //                    std::cout << "j_partner = " << j_partner << std::endl;
 298                     if ( abs(i_partner - j_partner) < 6){
 299                         if (i_partner < j_partner){
 300                             second_strand = i_partner;
 301                         }
 302                         else{
 303                             second_strand = j_partner;
 304                         }
 305                         for(int k{abs(i_partner - j_partner)}; k >= 0; --k){
 306                             SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Strand);
 307                             std::cout << second_strand + k << " is strand" << std::endl;
 308                         }
 309                         is_Estrand = true;
 310                     }
 311
 312                 }
 313             }
 314             if (is_Estrand){
 315                 for(std::size_t k{0}; k <= j; ++k){
 316                     SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Strand);
 317                     std::cout << i + k << " is strand" << std::endl;
 318                 }
 319                 break;
 320             }
 321         }
 322     }
 323
 324
 325
 326
 327
 328
 329
 330
 331
 332
 333
 334
 335 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 336 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 337 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 338 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 339 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 340 //                    Bridge[i].push_back(j);
 341 //                }
 342 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 343 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 344 //                    AntiBridge[i].push_back(j);
 345 //                }
 346 //            }
 347 //        }
 348 //    }
 349 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 350 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 351 //            setStatus(i, secondaryStructureTypes::Bulge);
 352 //        }
 353 //    }
 354 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 355 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 356 //            if (j == i){
 357 //                continue;
 358 //            }
 359 //            else {
 360 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 361 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 362 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 363 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 364 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 365 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 366 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 367 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 368 //                                        < 5)){
 369 //                                    if (j < i){
 370 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 371 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 372 //                                        }
 373 //                                    }
 374 //                                    else{
 375 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 376 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 377 //                                        }
 378 //                                    }
 379 //                                }
 380 //                            }
 381 //                        }
 382 //                    }
 383 //                }
 384 //            }
 385 //        }
 386 //    }
 387 }
 388
 389 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 390     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 391         std::size_t stride {static_cast<std::size_t>(i) + 3};
 392 //        std::cout << "Testing Helix_" << stride << std::endl;
 393         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 394 //            std::cout << "Testing " << j << " and " << j + stride << std::endl;
 395             if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
 396 //                std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 397                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 398
 399                 for (std::size_t k {1}; k < stride; ++k){
 400                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 401                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 402                         SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 403                     }
 404                 }
 405
 406                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 407                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 408                 }
 409                 else {
 410                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 411                 }
 412             }
 413         }
 414     }
 415
 416     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 417         std::size_t stride {static_cast<std::size_t>(i) + 3};
 418         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 419             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 420                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 421                 bool empty = true;
 422                 secondaryStructureTypes Helix;
 423                 switch(i){
 424                 case turnsTypes::Turn_3:
 425                     for (std::size_t k {0}; empty && k < stride; ++k){
 426                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 427                     }
 428                     Helix = secondaryStructureTypes::Helix_3;
 429                     break;
 430                 case turnsTypes::Turn_5:
 431                     for (std::size_t k {0}; empty && k < stride; ++k){
 432                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 433                     }
 434                     Helix = secondaryStructureTypes::Helix_5;
 435                     break;
 436                 default:
 437                     Helix = secondaryStructureTypes::Helix_4;
 438                     break;
 439                 }
 440                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 441                     for(std::size_t k {0}; k < stride; ++k ){
 442                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 443                     }
 444                 }
 445             }
 446         }
 447     }
 448
 449     /* Не знаю зач они в дссп так сделали, этож полное говно */
 450
 451 //    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 452 //        if (SecondaryStructuresStatusMap[i].getStatus() == secondaryStructureTypes::Loop || SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 453 //            bool isTurn = false;
 454 //            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 455 //                std::size_t stride {static_cast<std::size_t>(j) + 3};
 456 //                for(std::size_t k {1}; k < stride and !isTurn; ++k){
 457 //                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 458 //                }
 459 //            }
 460 //            if (isTurn){
 461 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 462 //            }
 463 //        }
 464 //    }
 465
 466 }
 467
 468 void secondaryStructures::analyzePPHelicesPatterns(){}
 469
 470 std::string secondaryStructures::patternSearch(){
 471
 472
 473     analyzeBridgesAndStrandsPatterns();
 474     analyzeTurnsAndHelicesPatterns();
 475 //    analyzePPHelicesPatterns();
 476
 477 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 478 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 479 //    }
 480
 481 //    std::cout.precision(5);
 482 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 483 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 484 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 485 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 486 //        }
 487 //        else {
 488 //            std::cout << " has no donor[0] and" ;
 489 //        }
 490 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 491 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 492 //        }
 493 //        else {
 494 //            std::cout << " has no acceptor[0]" ;
 495 //        }
 496 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 497 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 498 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 499 //        }
 500 //        else {
 501 //            std::cout << " has no donor[1] and" ;
 502 //        }
 503 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 504 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 505 //        }
 506 //        else {
 507 //            std::cout << " has no acceptor[1]" ;
 508 //        }
 509 //    }
 510
 511     /*Write Data*/
 512
 513     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 514         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 515             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 516                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 517             }
 518         }
 519     }
 520
 521     /*Add breaks*/
 522
 523     if(SecondaryStructuresStatusMap.size() > 1){
 524         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 525             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 526                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 527                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 528                     ++linefactor;
 529                 }
 530             }
 531         }
 532     }
 533     return SecondaryStructuresStringLine;
 534 }
 535
 536 secondaryStructures::~secondaryStructures(){
 537     SecondaryStructuresStatusMap.resize(0);
 538     SecondaryStructuresStringLine.resize(0);
 539 }
 540
 541 DsspTool::DsspStorage::DsspStorage(){
 542     storaged_data.resize(0);
 543 }
 544
 545 void DsspTool::DsspStorage::clearAll(){
 546     storaged_data.resize(0);
 547 }
 548
 549 std::mutex DsspTool::DsspStorage::mx;
 550
 551 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 552     std::lock_guard<std::mutex> guardian(mx);
 553     std::pair<int, std::string> datapair(frnr, data);
 554     storaged_data.push_back(datapair);
 555 }
 556
 557 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 558     std::sort(storaged_data.begin(), storaged_data.end());
 559     return storaged_data;
 560 }
 561
 562 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 563     cutoff = cutoff_init;
 564 }
 565
 566 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 567     while (coordinate < 0) {
 568         coordinate += vector_length;
 569     }
 570     while (coordinate >= vector_length) {
 571         coordinate -= vector_length;
 572     }
 573 }
 574
 575 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 576     if (x < 0) {
 577         x += x_max;
 578     }
 579     if (x >= x_max) {
 580         x -= x_max;
 581     }
 582 }
 583
 584 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 585     rvec coordinates, box_vector_length;
 586     num_of_miniboxes.resize(0);
 587     num_of_miniboxes.resize(3);
 588     for (std::size_t i{XX}; i <= ZZ; ++i) {
 589         box_vector_length[i] = std::sqrt(
 590                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 591         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 592     }
 593     MiniBoxesMap.resize(0);
 594     MiniBoxesReverseMap.resize(0);
 595     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 596                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 597                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 598                              0))));
 599     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 600     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 601         for (std::size_t j{XX}; j <= ZZ; ++j) {
 602             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 603             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 604         }
 605         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 606                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 607         for (std::size_t j{XX}; j <= ZZ; ++j){
 608             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 609         }
 610     }
 611 }
 612
 613 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 614     GetMiniBoxesMap(fr, IndexMap);
 615     MiniBoxSize[XX] = MiniBoxesMap.size();
 616     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 617     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 618     PairMap.resize(0);
 619     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 620     ResiI = PairMap.begin();
 621     ResiJ = ResiI->begin();
 622
 623     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 624         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 625             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 626                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 627                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 628                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 629                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 630                     }
 631                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 632                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 633                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 634                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 635                         }
 636                     }
 637                 }
 638             }
 639         }
 640     }
 641 }
 642
 643 bool alternateNeighborhoodSearch::findNextPair(){
 644
 645     if(!PairMap.size()){
 646         return false;
 647     }
 648
 649     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 650         for(; ResiJ != ResiI->end(); ++ResiJ){
 651             if(*ResiJ){
 652                 resiIpos = ResiI - PairMap.begin();
 653                 resiJpos = ResiJ - ResiI->begin();
 654                 if ( ResiJ != ResiI->end() ){
 655                     ++ResiJ;
 656                 }
 657                 else if (ResiI != PairMap.end()) {
 658                     ++ResiI;
 659                     ResiJ = ResiI->begin();
 660                 }
 661                 else {
 662                     return false; // ???
 663                 }
 664                 return true;
 665             }
 666         }
 667     }
 668
 669     return false;
 670 }
 671
 672 std::size_t alternateNeighborhoodSearch::getResiI() const {
 673     return resiIpos;
 674 }
 675
 676 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 677     return resiJpos;
 678 }
 679
 680
 681 DsspTool::DsspStorage DsspTool::Storage;
 682
 683 DsspTool::DsspTool(){
 684 }
 685
 686 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 687 {
 688    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 689    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 690    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 691    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 692    {
 693        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 694                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 695                                     fr,
 696                                     pbc)
 697            > maxdist)
 698        {
 699            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 700            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 701
 702 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 703        }
 704    }
 705    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 706    {
 707        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 708            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 709            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 710            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 711           )
 712        {
 713            continue;
 714        }
 715        for (int j{ 0 }; j < 3; ++j)
 716        {
 717            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 718                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 719            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 720                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 721        }
 722        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 723        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 724                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 725                                         fr,
 726                                         pbc)
 727                * gmx::c_angstrom / gmx::c_nano
 728                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 729                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 730                                           fr,
 731                                           pbc)
 732                * gmx::c_angstrom / gmx::c_nano;
 733        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 734        if (degree > benddegree)
 735        {
 736            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 737        }
 738    }
 739 }
 740
 741 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 742                        ResInfo& Acceptor,
 743                        const t_trxframe&          fr,
 744                        const t_pbc*               pbc)
 745 {
 746    /*
 747     * DSSP uses eq from dssp 2.x
 748     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 749     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 750     * if R is in A
 751     * Hbond if E < -0.5
 752     *
 753     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 754     *
 755     */
 756
 757     if (CalculateAtomicDistances(
 758                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 759         >= minimalCAdistance)
 760     {
 761         return void();
 762     }
 763
 764     const float kCouplingConstant = 27.888;
 765     const float minimalAtomDistance{ 0.5 },
 766             minEnergy{ -9.9 };
 767     float HbondEnergy{ 0 };
 768     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 769
 770 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 771
 772     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 773                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 774         distanceNO = CalculateAtomicDistances(
 775                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 776         distanceNC = CalculateAtomicDistances(
 777                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 778         if (initParams.addHydrogens){
 779             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 780                rvec atomH{};
 781                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 782                for (int i{XX}; i <= ZZ; ++i){
 783                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 784                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 785                    atomH[i] += prevCO / prevCODist;
 786                }
 787                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 788                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 789             }
 790             else{
 791                 distanceHO = distanceNO;
 792                 distanceHC = distanceNC;
 793             }
 794        }
 795        else {
 796            distanceHO = CalculateAtomicDistances(
 797                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 798            distanceHC = CalculateAtomicDistances(
 799                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 800        }
 801        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 802         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 803        {
 804             HbondEnergy = minEnergy;
 805        }
 806        else{
 807            HbondEnergy =
 808                    kCouplingConstant
 809                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 810        }
 811
 812 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 813 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 814 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 815 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 816 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 817 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 818
 819        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 820
 821 //       if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
 822 //            HbondEnergy = minEnergy;
 823 //       }
 824
 825 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 826     }
 827 //    else{
 828 //        std::cout << "Donor Is Proline" << std::endl;
 829 //    }
 830
 831     if (HbondEnergy < Donor.acceptorEnergy[0]){
 832            Donor.acceptor[1] = Donor.acceptor[0];
 833            Donor.acceptor[0] = Acceptor.info;
 834            Donor.acceptorEnergy[0] = HbondEnergy;
 835     }
 836     else if (HbondEnergy < Donor.acceptorEnergy[1]){
 837            Donor.acceptor[1] = Acceptor.info;
 838            Donor.acceptorEnergy[1] = HbondEnergy;
 839     }
 840
 841     if (HbondEnergy < Acceptor.donorEnergy[0]){
 842            Acceptor.donor[1] = Acceptor.donor[0];
 843            Acceptor.donor[0] = Donor.info;
 844            Acceptor.donorEnergy[0] = HbondEnergy;
 845     }
 846     else if (HbondEnergy < Acceptor.donorEnergy[1]){
 847            Acceptor.donor[1] = Donor.info;
 848            Acceptor.donorEnergy[1] = HbondEnergy;
 849     }
 850 }
 851
 852
 853 /* Calculate Distance From B to A */
 854 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 855 {
 856    gmx::RVec r{ 0, 0, 0 };
 857    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 858    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 859 }
 860
 861 /* Calculate Distance From B to A, where A is only fake coordinates */
 862 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 863 {
 864    gmx::RVec r{ 0, 0, 0 };
 865    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 866    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 867 }
 868
 869 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 870 {
 871    initParams = initParamz;
 872    ResInfo _backboneAtoms;
 873    std::size_t                 i{ 0 };
 874    std::string proLINE;
 875    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
 876    IndexMap.resize(0);
 877    IndexMap.push_back(_backboneAtoms);
 878    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 879    proLINE = *(IndexMap[i].info->name);
 880    if( proLINE.compare("PRO") == 0 ){
 881        IndexMap[i].is_proline = true;
 882    }
 883
 884    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
 885        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
 886        {
 887            ++i;
 888            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
 889            IndexMap.emplace_back(_backboneAtoms);
 890            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 891            proLINE = *(IndexMap[i].info->name);
 892            if( proLINE.compare("PRO") == 0 ){
 893                IndexMap[i].is_proline = true;
 894            }
 895
 896        }
 897        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
 898        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
 899        {
 900            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
 901        }
 902        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
 903        {
 904            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
 905        }
 906        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
 907        {
 908            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
 909        }
 910        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
 911        {
 912            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
 913            if (initParamz.addHydrogens == true){
 914                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 915            }
 916        }
 917        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 918        {
 919            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 920        }
 921
 922
 923
 924 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 925 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 926 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 927 //       }
 928    }
 929
 930    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 931        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 932
 933        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 934
 935 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 936 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 937 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 938 //         std::cout << IndexMap[j].prevResi->info->nr;
 939 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 940 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 941 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 942 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 943 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 944 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 945    }
 946
 947    nres = i + 1;
 948 }
 949
 950 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 951 {
 952
 953     switch(initParams.NBS){
 954     case (NBSearchMethod::Classique): {
 955
 956         // store positions of CA atoms to use them for nbSearch
 957         std::vector<gmx::RVec> positionsCA_;
 958         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 959         {
 960             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 961         }
 962
 963         AnalysisNeighborhood nb_;
 964         nb_.setCutoff(initParams.cutoff_);
 965         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 966         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 967         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 968         gmx::AnalysisNeighborhoodPair       pair;
 969         while (pairSearch.findNextPair(&pair))
 970         {
 971             if(CalculateAtomicDistances(
 972                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 973                 < minimalCAdistance){
 974                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 975                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 976                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 977                 }
 978             }
 979         }
 980
 981         break;
 982     }
 983     case (NBSearchMethod::Experimental): { // TODO FIX
 984
 985         alternateNeighborhoodSearch as_;
 986
 987         as_.setCutoff(initParams.cutoff_);
 988
 989         as_.AltPairSearch(fr, IndexMap);
 990
 991         while (as_.findNextPair()){
 992             if(CalculateAtomicDistances(
 993                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 994                 < minimalCAdistance){
 995                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 996                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 997                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 998                 }
 999             }
1000         }
1001
1002         break;
1003     }
1004     default: {
1005
1006         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
1007             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
1008                 if(CalculateAtomicDistances(
1009                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1010                     < minimalCAdistance){
1011                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
1012                     if (Acceptor != Donor + 1){
1013                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
1014                     }
1015                 }
1016             }
1017         }
1018         break;
1019     }
1020     }
1021
1022
1023 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
1024 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
1025 //    }
1026
1027    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
1028    calculateBends(fr, pbc);
1029    Storage.storageData(frnr, PatternSearch.patternSearch());
1030
1031 }
1032
1033 std::vector<std::pair<int, std::string>> DsspTool::getData(){
1034     return Storage.returnData();
1035 }
1036
1037 } // namespace analysismodules
1038
1039 } // namespace gmx