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,
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   7 * top-level source directory and at http://www.gromacs.org.
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  35 /*! \internal \file
  36 * \brief
  37 * Implements gmx::analysismodules::Trajectory.
  38 *
  39 * \author Sergey Gorelov <Infinity2573@gmail.com>
  40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
  41 * \author Alexey Shvetsov <alexxyum@gmail.com>
  42 * \ingroup module_trajectoryanalysis
  43 */
  44
  45 #include "dssptools.h"
  46
  47 #include <algorithm>
  48 #include "gromacs/math/units.h"
  49
  50 #include "gromacs/pbcutil/pbc.h"
  51 #include <gromacs/trajectoryanalysis.h>
  52 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  53 #include <set>
  54 #include <fstream>
  55 #include <mutex>
  56 #include <iostream>
  57
  58 namespace gmx
  59 {
  60
  61 namespace analysismodules
  62 {
  63
  64 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
  65 //{
  66 //   _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
  67 //}
  68
  69 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
  70 //{
  71 //   return _ResInfo[static_cast<std::size_t>(atomTypeName)];
  72 //}
  73
  74 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
  75     return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
  76 }
  77
  78 secondaryStructures::secondaryStructures(){
  79 }
  80 void secondaryStructures::initiateSearch(const std::vector<ResInfo> &ResInfoMatrix, const bool PiHelicesPreferencez, const int _pp_stretch){
  81     SecondaryStructuresStatusMap.resize(0);
  82     SecondaryStructuresStringLine.resize(0);
  83     std::vector<std::size_t> temp; temp.resize(0),
  84     PiHelixPreference = PiHelicesPreferencez;
  85     ResInfoMap = &ResInfoMatrix;
  86     pp_stretch = _pp_stretch;
  87     SecondaryStructuresStatusMap.resize(ResInfoMatrix.size());
  88     SecondaryStructuresStringLine.resize(ResInfoMatrix.size(), '~');
  89 }
  90
  91 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName, bool status){
  92     SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = status;
  93     if (status){
  94         SecondaryStructuresStatus = secondaryStructureTypeName;
  95     }
  96     else{
  97         SecondaryStructuresStatus = secondaryStructureTypes::Loop;
  98     }
  99 }
 100
 101 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
 102     TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
 103 }
 104
 105 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
 106     return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
 107 }
 108
 109 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
 110     return breakPartners[0] == partner || breakPartners[1] == partner;
 111 }
 112
 113 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
 114     return TurnsStatusArray[static_cast<std::size_t>(turn)];
 115 }
 116
 117 secondaryStructureTypes secondaryStructures::secondaryStructuresData::getStatus() const{
 118     return  SecondaryStructuresStatus;
 119 }
 120
 121 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
 122     if (breakPartners[0] == nullptr){
 123         breakPartners[0] = breakPartner;
 124     }
 125     else{
 126         breakPartners[1] = breakPartner;
 127     }
 128     setStatus(secondaryStructureTypes::Break);
 129 }
 130
 131 void secondaryStructures::secondaryStructuresData::setBridge(secondaryStructuresData *bridgePartner, std::size_t bridgePartnerIndex, bridgeTypes bridgeType){
 132     if(bridgeType == bridgeTypes::ParallelBridge){
 133         bridgePartners[0] = bridgePartner;
 134         bridgePartnersIndexes[0] = bridgePartnerIndex;
 135     }
 136     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 137         bridgePartners[1] = bridgePartner;
 138         bridgePartnersIndexes[1] = bridgePartnerIndex;
 139     }
 140 }
 141
 142 bool secondaryStructures::secondaryStructuresData::hasBridges() const{
 143     return bridgePartners[0] || bridgePartners[1];
 144
 145 }
 146
 147 bool secondaryStructures::secondaryStructuresData::hasBridges(bridgeTypes bridgeType) const{
 148     if(bridgeType == bridgeTypes::ParallelBridge){
 149         return bridgePartners[0] != nullptr;
 150     }
 151     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 152         return bridgePartners[1] != nullptr;
 153     }
 154
 155     return false;
 156
 157 }
 158
 159 bool secondaryStructures::secondaryStructuresData::isBridgePartnerWith(secondaryStructuresData *bridgePartner, bridgeTypes bridgeType) const{
 160     if(bridgeType == bridgeTypes::ParallelBridge){
 161         return bridgePartners[0] == bridgePartner;
 162     }
 163     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 164         return bridgePartners[1] == bridgePartner;
 165     }
 166     return false;
 167 }
 168
 169 std::size_t secondaryStructures::secondaryStructuresData::getBridgePartnerIndex(bridgeTypes bridgeType) const{
 170     if (bridgeType == bridgeTypes::ParallelBridge){
 171         return bridgePartnersIndexes[0];
 172     }
 173     return bridgePartnersIndexes[1];
 174 }
 175
 176 secondaryStructures::secondaryStructuresData secondaryStructures::secondaryStructuresData::getBridgePartner(bridgeTypes bridgeType) const{
 177     if(bridgeType == bridgeTypes::ParallelBridge){
 178         return *(bridgePartners[0]);
 179     }
 180     return *(bridgePartners[1]);
 181 }
 182
 183 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
 184 //    if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
 185 //        (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
 186 //        (*ResInfoMap)[Acceptor].info == nullptr ){
 187 //        std::cout << "Bad hbond check. Reason(s): " ;
 188 //        if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 189 //            std::cout << "Donor has no acceptor[0]; ";
 190 //        }
 191 //        if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 192 //            std::cout << "Donor has no acceptor[1]; ";
 193 //        }
 194 //        if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 195 //            std::cout << "No info about acceptor; ";
 196 //        }
 197 //        std::cout << std::endl;
 198 //        return false;
 199 //    }
 200 //    else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
 201 //              (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
 202 //              (*ResInfoMap)[Donor].info == nullptr )) {
 203 //        std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
 204 //        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;
 205 //        std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
 206 //        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;
 207 //        std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
 208 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 209 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 210 //            std::cout << "HBond Exist" << std::endl;
 211 //        }
 212 //    }
 213 //    else {
 214 //        std::cout << "Bad hbond check. Reason(s): " ;
 215 //        if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
 216 //            std::cout << "Acceptor has no donor[0]; ";
 217 //        }
 218 //        if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
 219 //            std::cout << "Acceptor has no donor[1]; ";
 220 //        }
 221 //        if ( (*ResInfoMap)[Donor].info == nullptr ){
 222 //            std::cout << "No info about donor; ";
 223 //        }
 224 //        std::cout << std::endl;
 225 //    }
 226
 227     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 228            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 229
 230
 231 }
 232
 233 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 234     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 235     if ( i > j ){
 236         std::swap(i, j);
 237     }
 238
 239     for (; i != j; ++i){
 240         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 241 //            std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 242             return false;
 243         }
 244     }
 245     return true;
 246 }
 247
 248 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 249     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){ // Protection from idiotz, не обязательно нужен
 250         return bridgeTypes::None;
 251     }
 252
 253     ResInfo a{(*ResInfoMap)[i]}, b{(*ResInfoMap)[j]};
 254
 255     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1) && a.prevResi && a.nextResi && b.prevResi && b.nextResi){
 256         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){
 257             return bridgeTypes::ParallelBridge;
 258         }
 259         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){
 260             return bridgeTypes::AntiParallelBridge;
 261         }
 262     }
 263     return bridgeTypes::None;
 264 }
 265
 266 void secondaryStructures::analyzeBridgesAndStrandsPatterns(){
 267 //  Calculate Bridgez
 268     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 269         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 270             switch(calculateBridge(i, j)){
 271             case bridgeTypes::ParallelBridge : {
 272                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::ParallelBridge);
 273                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 274                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::ParallelBridge);
 275                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 276             }
 277             case bridgeTypes::AntiParallelBridge : {
 278                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::AntiParallelBridge);
 279                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 280                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::AntiParallelBridge);
 281                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 282             }
 283             default :
 284                 continue;
 285             }
 286         }
 287     }
 288 //  Calculate Extended Strandz
 289     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 290         bool is_Estrand {false};
 291         for(std::size_t j {2}; j != 0; --j){
 292             for(const bridgeTypes &bridgeType : {bridgeTypes::ParallelBridge, bridgeTypes::AntiParallelBridge}){
 293                 if (SecondaryStructuresStatusMap[i].hasBridges(bridgeType) && SecondaryStructuresStatusMap[i + j].hasBridges(bridgeType) ){
 294                     std::size_t i_partner{SecondaryStructuresStatusMap[i].getBridgePartnerIndex(bridgeType)}, j_partner{SecondaryStructuresStatusMap[i + j].getBridgePartnerIndex(bridgeType)}, second_strand{};
 295                     if ( abs(i_partner - j_partner) < 6){
 296                         if (i_partner < j_partner){
 297                             second_strand = i_partner;
 298                         }
 299                         else{
 300                             second_strand = j_partner;
 301                         }
 302                         for(int k{abs(i_partner - j_partner)}; k >= 0; --k){
 303                             if (SecondaryStructuresStatusMap[second_strand + k].getStatus(secondaryStructureTypes::Bridge)){
 304                                 SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Bridge, false);
 305                             }
 306
 307                             SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Strand);
 308                         }
 309                         is_Estrand = true;
 310                     }
 311                 }
 312             }
 313             if (is_Estrand){
 314                 for(std::size_t k{0}; k <= j; ++k){
 315                     if (SecondaryStructuresStatusMap[i + k].getStatus(secondaryStructureTypes::Bridge)){
 316                         SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Bridge, false);
 317                     }
 318                     SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Strand);
 319                 }
 320                 break;
 321             }
 322         }
 323     }
 324
 325
 326
 327
 328
 329
 330
 331
 332
 333
 334
 335
 336 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 337 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 338 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 339 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 340 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 341 //                    Bridge[i].push_back(j);
 342 //                }
 343 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 344 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 345 //                    AntiBridge[i].push_back(j);
 346 //                }
 347 //            }
 348 //        }
 349 //    }
 350 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 351 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 352 //            setStatus(i, secondaryStructureTypes::Bulge);
 353 //        }
 354 //    }
 355 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 356 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 357 //            if (j == i){
 358 //                continue;
 359 //            }
 360 //            else {
 361 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 362 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 363 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 364 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 365 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 366 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 367 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 368 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 369 //                                        < 5)){
 370 //                                    if (j < i){
 371 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 372 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 373 //                                        }
 374 //                                    }
 375 //                                    else{
 376 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 377 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 378 //                                        }
 379 //                                    }
 380 //                                }
 381 //                            }
 382 //                        }
 383 //                    }
 384 //                }
 385 //            }
 386 //        }
 387 //    }
 388 }
 389
 390 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 391     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 392         std::size_t stride {static_cast<std::size_t>(i) + 3};
 393         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 394             if (hasHBondBetween(j + stride, j)){
 395                             std::cout << "Bond between " << j << " and " << j + stride << " exists" << std::endl;
 396                         }
 397             if (!NoChainBreaksBetween(j, j + stride)){
 398                             std::cout << "ChainBreak between " << j << " and " << j + stride << std::endl;
 399                         }
 400             if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
 401 //                std::cout << "Resi " << j << " is Helix_" << stride << " start" << std::endl;
 402                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 403
 404                 for (std::size_t k {1}; k < stride; ++k){
 405                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 406                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 407 //                        SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 408                     }
 409                 }
 410
 411                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 412                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 413                 }
 414                 else {
 415                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 416                 }
 417             }
 418         }
 419     }
 420
 421     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 422         std::size_t stride {static_cast<std::size_t>(i) + 3};
 423         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 424             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 425                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 426                 bool empty = true;
 427                 secondaryStructureTypes Helix;
 428                 switch(i){
 429                 case turnsTypes::Turn_3:
 430                     for (std::size_t k {0}; empty && k < stride; ++k){
 431                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 432                     }
 433                     Helix = secondaryStructureTypes::Helix_3;
 434                     break;
 435                 case turnsTypes::Turn_5:
 436                     for (std::size_t k {0}; empty && k < stride; ++k){
 437                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 438                     }
 439                     Helix = secondaryStructureTypes::Helix_5;
 440                     break;
 441                 default:
 442                     Helix = secondaryStructureTypes::Helix_4;
 443                     break;
 444                 }
 445                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 446                     for(std::size_t k {0}; k < stride; ++k ){
 447 //                        std::cout << "Resi " << j << " is Helix_" << static_cast<std::size_t>(Helix) - 5 << std::endl;
 448                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 449                     }
 450                 }
 451             }
 452         }
 453     }
 454
 455     /* Не знаю зач они в дссп так сделали, этож полное говно */
 456
 457     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 458         if (static_cast<int>(SecondaryStructuresStatusMap[i].getStatus()) <= static_cast<int>(secondaryStructureTypes::Turn)){
 459             bool isTurn = false;
 460             for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 461                 std::size_t stride {static_cast<std::size_t>(j) + 3};
 462                 for(std::size_t k {1}; k < stride and !isTurn; ++k){
 463                     isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 464                 }
 465             }
 466             if (isTurn){
 467 //                std::cout << "Resi " << i << " is Turn" << std::endl;
 468                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 469             }
 470         }
 471     }
 472
 473 }
 474
 475 std::string secondaryStructures::patternSearch(){
 476
 477
 478     analyzeBridgesAndStrandsPatterns();
 479     analyzeTurnsAndHelicesPatterns();
 480
 481 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 482 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 483 //    }
 484
 485 //    std::cout.precision(5);
 486 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 487 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 488 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 489 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 490 //        }
 491 //        else {
 492 //            std::cout << " has no donor[0] and" ;
 493 //        }
 494 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 495 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 496 //        }
 497 //        else {
 498 //            std::cout << " has no acceptor[0]" ;
 499 //        }
 500 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 501 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 502 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 503 //        }
 504 //        else {
 505 //            std::cout << " has no donor[1] and" ;
 506 //        }
 507 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 508 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 509 //        }
 510 //        else {
 511 //            std::cout << " has no acceptor[1]" ;
 512 //        }
 513 //    }
 514
 515     /*Write Data*/
 516
 517     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 518         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 519             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 520                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 521             }
 522         }
 523     }
 524
 525     /*Add breaks*/
 526
 527     if(SecondaryStructuresStatusMap.size() > 1){
 528         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 529             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 530                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 531                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 532                     ++linefactor;
 533                 }
 534             }
 535         }
 536     }
 537     return SecondaryStructuresStringLine;
 538 }
 539
 540 secondaryStructures::~secondaryStructures(){
 541     SecondaryStructuresStatusMap.resize(0);
 542     SecondaryStructuresStringLine.resize(0);
 543 }
 544
 545 DsspTool::DsspStorage::DsspStorage(){
 546     storaged_data.resize(0);
 547 }
 548
 549 void DsspTool::DsspStorage::clearAll(){
 550     storaged_data.resize(0);
 551 }
 552
 553 std::mutex DsspTool::DsspStorage::mx;
 554
 555 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 556     std::lock_guard<std::mutex> guardian(mx);
 557     std::pair<int, std::string> datapair(frnr, data);
 558     storaged_data.push_back(datapair);
 559 }
 560
 561 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 562     std::sort(storaged_data.begin(), storaged_data.end());
 563     return storaged_data;
 564 }
 565
 566 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 567     cutoff = cutoff_init;
 568 }
 569
 570 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 571     while (coordinate < 0) {
 572         coordinate += vector_length;
 573     }
 574     while (coordinate >= vector_length) {
 575         coordinate -= vector_length;
 576     }
 577 }
 578
 579 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 580     if (x < 0) {
 581         x += x_max;
 582     }
 583     if (x >= x_max) {
 584         x -= x_max;
 585     }
 586 }
 587
 588 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 589     rvec coordinates, box_vector_length;
 590     num_of_miniboxes.resize(0);
 591     num_of_miniboxes.resize(3);
 592     for (std::size_t i{XX}; i <= ZZ; ++i) {
 593         box_vector_length[i] = std::sqrt(
 594                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 595         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 596     }
 597     MiniBoxesMap.resize(0);
 598     MiniBoxesReverseMap.resize(0);
 599     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 600                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 601                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 602                              0))));
 603     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 604     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 605         for (std::size_t j{XX}; j <= ZZ; ++j) {
 606             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 607             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 608         }
 609         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 610                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 611         for (std::size_t j{XX}; j <= ZZ; ++j){
 612             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 613         }
 614     }
 615 }
 616
 617 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 618     GetMiniBoxesMap(fr, IndexMap);
 619     MiniBoxSize[XX] = MiniBoxesMap.size();
 620     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 621     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 622     PairMap.resize(0);
 623     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 624     ResiI = PairMap.begin();
 625     ResiJ = ResiI->begin();
 626
 627     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 628         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 629             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 630                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 631                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 632                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 633                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 634                     }
 635                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 636                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 637                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 638                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 639                         }
 640                     }
 641                 }
 642             }
 643         }
 644     }
 645 }
 646
 647 bool alternateNeighborhoodSearch::findNextPair(){
 648
 649     if(!PairMap.size()){
 650         return false;
 651     }
 652
 653     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 654         for(; ResiJ != ResiI->end(); ++ResiJ){
 655             if(*ResiJ){
 656                 resiIpos = ResiI - PairMap.begin();
 657                 resiJpos = ResiJ - ResiI->begin();
 658                 if ( ResiJ != ResiI->end() ){
 659                     ++ResiJ;
 660                 }
 661                 else if (ResiI != PairMap.end()) {
 662                     ++ResiI;
 663                     ResiJ = ResiI->begin();
 664                 }
 665                 else {
 666                     return false; // ???
 667                 }
 668                 return true;
 669             }
 670         }
 671     }
 672
 673     return false;
 674 }
 675
 676 std::size_t alternateNeighborhoodSearch::getResiI() const {
 677     return resiIpos;
 678 }
 679
 680 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 681     return resiJpos;
 682 }
 683
 684
 685 DsspTool::DsspStorage DsspTool::Storage;
 686
 687 DsspTool::DsspTool(){
 688 }
 689
 690 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 691 {
 692    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 693    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 694    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 695    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 696    {
 697        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 698                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 699                                     fr,
 700                                     pbc)
 701            > maxdist)
 702        {
 703            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 704            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 705
 706 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 707        }
 708    }
 709    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 710    {
 711        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 712            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 713            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 714            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 715           )
 716        {
 717            continue;
 718        }
 719        for (int j{ 0 }; j < 3; ++j)
 720        {
 721            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 722                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 723            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 724                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 725        }
 726        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 727        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 728                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 729                                         fr,
 730                                         pbc)
 731                * gmx::c_angstrom / gmx::c_nano
 732                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 733                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 734                                           fr,
 735                                           pbc)
 736                * gmx::c_angstrom / gmx::c_nano;
 737        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 738        if (degree > benddegree)
 739        {
 740            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 741        }
 742    }
 743 }
 744
 745 float DsspTool::CalculateDihedralAngle(const int &A, const int &B, const int &C, const int &D, const t_trxframe &fr, const t_pbc *pbc){
 746     float result{360}, u{}, v{};
 747     gmx::RVec v12{}, v43{}, z{}, p{}, x{}, y{};
 748     pbc_dx(pbc, fr.x[A], fr.x[B], v12.as_vec());
 749     pbc_dx(pbc, fr.x[D], fr.x[C], v43.as_vec());
 750     pbc_dx(pbc, fr.x[B], fr.x[C], z.as_vec());
 751
 752     for(std::size_t j {XX}; j <= ZZ; ++j){
 753         v12[j] *= gmx::c_nm2A;
 754         v43[j] *= gmx::c_nm2A;
 755         z[j] *= gmx::c_nm2A;
 756     }
 757     for(std::size_t i{XX}, j{j + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
 758         if (j > 2){
 759             j -= 3;
 760         }
 761         if (k > 2){
 762             k -= 3;
 763         }
 764         p[i] = (z[j] * v12[k]) - (z[k] * v12[j]);
 765         x[i] = (z[j] * v43[k]) - (z[k] * v43[j]);
 766
 767     }
 768     for(std::size_t i{XX}, j{j + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
 769         if (j > 2){
 770             j -= 3;
 771         }
 772         if (k > 2){
 773             k -= 3;
 774         }
 775         y[i] = (z[j] * x[k]) - (z[k] * x[j]);
 776     }
 777
 778 //    std::cout << "v12 = " << v12[0] << ", " << v12[1] << ", " << v12[2] << std::endl;
 779 //    std::cout << "v43 = " << v43[0] << ", " << v43[1] << ", " << v43[2] << std::endl;
 780 //    std::cout << "z = " << z[0] << ", " << z[1] << ", " << z[2] << std::endl;
 781 //    std::cout << "p = " << p[0] << ", " << p[1] << ", " << p[2] << std::endl;
 782 //    std::cout << "x = " << x[0] << ", " << x[1] << ", " << x[2] << std::endl;
 783 //    std::cout << "y = " << y[0] << ", " << y[1] << ", " << y[2] << std::endl;
 784
 785     u = (x[XX] * x[XX]) + (x[YY] * x[YY]) + (x[ZZ] * x[ZZ]);
 786     v = (y[XX] * y[XX]) + (y[YY] * y[YY]) + (y[ZZ] * y[ZZ]);
 787
 788 //    std::cout << "u = " << u << std::endl;
 789 //    std::cout << "v = " << v << std::endl;
 790
 791     if (u > 0 and v > 0){
 792         u = ((p[XX] * x[XX]) + (p[YY] * x[YY]) + (p[ZZ] * x[ZZ])) / std::sqrt(u);
 793         v = ((p[XX] * y[XX]) + (p[YY] * y[YY]) + (p[ZZ] * y[ZZ])) / std::sqrt(v);
 794 //        std::cout << "new u = " << u << std::endl;
 795 //        std::cout << "new v = " << v << std::endl;
 796         if (u != 0 or v != 0){
 797             result = std::atan2(v, u) * gmx::c_rad2Deg;
 798 //            std::cout << "result = " << result << std::endl;
 799         }
 800     }
 801     return result;
 802 }
 803
 804 void DsspTool::calculateDihedrals(const t_trxframe &fr, const t_pbc *pbc){
 805     const float epsilon = 29;
 806     const float phi_min = -75 - epsilon; // -104
 807     const float phi_max = -75 + epsilon; // -46
 808     const float psi_min = 145 - epsilon; // 116
 809     const float psi_max = 145 + epsilon; // 176
 810     std::vector<float>          phi(IndexMap.size(), 360), psi(IndexMap.size(), 360);
 811 //    phi.resize(0);
 812 //    psi.resize(0);
 813 //    phi.resize(IndexMap.size(), 360);
 814 //    psi.resize(IndexMap.size(), 360);
 815
 816     for (std::size_t i = 1; i + 1 < IndexMap.size(); ++i){ // TODO add index verifictaion (check if those atom indexes exist)
 817 //        std::cout << "For resi " << i << " :" << std::endl;
 818         phi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i - 1].getIndex(backboneAtomTypes::AtomC)),
 819                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
 820                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
 821                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 822                                         fr,
 823                                         pbc);
 824         psi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
 825                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
 826                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 827                                         static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 828                                         fr,
 829                                         pbc);
 830 //        std::cout << "For " << i << " phi = " << phi[i] << ", psi = " << psi[i] << std::endl;
 831 //        std::cout << "phi[" << i << "] = " << phi[i] << std::endl;
 832 //        std::cout << "psi[" << i << "] = " << psi[i] << std::endl;
 833     }
 834
 835     for (std::size_t i = 1; i + 3 < IndexMap.size(); ++i){
 836         switch (initParams.pp_stretch){
 837         case 2: {
 838             if (phi_min > phi[i] or phi[i] > phi_max or
 839                 phi_min > phi[i + 1] or phi[i + 1]> phi_max){
 840                 continue;
 841             }
 842
 843             if (psi_min > psi[i] or psi[i] > psi_max or
 844                 psi_min > psi[i + 1] or psi[i + 1] > psi_max){
 845                 continue;
 846             }
 847
 848             switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
 849                 case HelixPositions::None:
 850                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
 851                     break;
 852
 853                 case HelixPositions::End:
 854                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
 855                     break;
 856
 857                 default:
 858                     break;
 859             }
 860
 861             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
 862             /* Пропустил проверку того, что заменяемая ак - петля */
 863             PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
 864             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
 865             break;
 866         }
 867         case 3:{
 868             if (phi_min > phi[i] or phi[i] > phi_max or
 869                 phi_min > phi[i + 1] or phi[i + 1]> phi_max or
 870                 phi_min > phi[i + 2] or phi[i + 2]> phi_max){
 871                 continue;
 872             }
 873
 874             if (psi_min > psi[i] or psi[i] > psi_max or
 875                 psi_min > psi[i + 1] or psi[i + 1] > psi_max or
 876                 psi_min > psi[i + 2] or psi[i + 2] > psi_max){
 877                 continue;
 878             }
 879
 880             switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
 881                 case HelixPositions::None:
 882                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
 883                     break;
 884
 885                 case HelixPositions::End:
 886                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
 887                     break;
 888
 889                 default:
 890                     break;
 891             }
 892
 893             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::Middle, turnsTypes::Turn_PP);
 894             PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
 895             /* Пропустил проверку того, что заменяемая ак - петля */
 896             PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
 897             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
 898             PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(secondaryStructureTypes::Helix_PP);
 899
 900             break;
 901         }
 902         default:
 903             throw std::runtime_error("Unsupported stretch length");
 904         }
 905     }
 906
 907 }
 908
 909 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 910                        ResInfo& Acceptor,
 911                        const t_trxframe&          fr,
 912                        const t_pbc*               pbc)
 913 {
 914    /*
 915     * DSSP uses eq from dssp 2.x
 916     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 917     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 918     * if R is in A
 919     * Hbond if E < -0.5
 920     *
 921     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 922     *
 923     */
 924
 925     if (CalculateAtomicDistances(
 926                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 927         >= minimalCAdistance)
 928     {
 929         return void();
 930     }
 931
 932     const float kCouplingConstant = 27.888;
 933     const float minimalAtomDistance{ 0.5 },
 934             minEnergy{ -9.9 };
 935     float HbondEnergy{ 0 };
 936     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 937
 938 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 939
 940     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 941                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 942         distanceNO = CalculateAtomicDistances(
 943                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 944         distanceNC = CalculateAtomicDistances(
 945                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 946         if (initParams.addHydrogens){
 947             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 948                rvec atomH{};
 949                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 950                for (int i{XX}; i <= ZZ; ++i){
 951                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 952                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 953                    atomH[i] += prevCO / prevCODist;
 954                }
 955                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 956                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 957             }
 958             else{
 959                 distanceHO = distanceNO;
 960                 distanceHC = distanceNC;
 961             }
 962        }
 963        else {
 964            distanceHO = CalculateAtomicDistances(
 965                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 966            distanceHC = CalculateAtomicDistances(
 967                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 968        }
 969        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 970         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 971        {
 972             HbondEnergy = minEnergy;
 973        }
 974        else{
 975            HbondEnergy =
 976                    kCouplingConstant
 977                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 978        }
 979
 980 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 981 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 982 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 983 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 984 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 985 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 986
 987        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 988
 989        if ( HbondEnergy < minEnergy ){
 990             HbondEnergy = minEnergy;
 991        }
 992
 993 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 994     }
 995 //    else{
 996 //        std::cout << "Donor Is Proline" << std::endl;
 997 //    }
 998
 999     if (HbondEnergy < Donor.acceptorEnergy[0]){
1000            Donor.acceptor[1] = Donor.acceptor[0];
1001            Donor.acceptor[0] = Acceptor.info;
1002            Donor.acceptorEnergy[0] = HbondEnergy;
1003     }
1004     else if (HbondEnergy < Donor.acceptorEnergy[1]){
1005            Donor.acceptor[1] = Acceptor.info;
1006            Donor.acceptorEnergy[1] = HbondEnergy;
1007     }
1008
1009     if (HbondEnergy < Acceptor.donorEnergy[0]){
1010            Acceptor.donor[1] = Acceptor.donor[0];
1011            Acceptor.donor[0] = Donor.info;
1012            Acceptor.donorEnergy[0] = HbondEnergy;
1013     }
1014     else if (HbondEnergy < Acceptor.donorEnergy[1]){
1015            Acceptor.donor[1] = Donor.info;
1016            Acceptor.donorEnergy[1] = HbondEnergy;
1017     }
1018 }
1019
1020
1021 /* Calculate Distance From B to A */
1022 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1023 {
1024    gmx::RVec r{ 0, 0, 0 };
1025    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
1026    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1027 }
1028
1029 /* Calculate Distance From B to A, where A is only fake coordinates */
1030 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1031 {
1032    gmx::RVec r{ 0, 0, 0 };
1033    pbc_dx(pbc, A, fr.x[B], r.as_vec());
1034    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1035 }
1036
1037 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
1038 {
1039    initParams = initParamz;
1040    ResInfo _backboneAtoms;
1041    std::size_t                 i{ 0 };
1042    std::string proLINE;
1043    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
1044    IndexMap.resize(0);
1045    IndexMap.push_back(_backboneAtoms);
1046    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1047    proLINE = *(IndexMap[i].info->name);
1048    if( proLINE.compare("PRO") == 0 ){
1049        IndexMap[i].is_proline = true;
1050    }
1051
1052    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
1053        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
1054        {
1055            ++i;
1056            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
1057            IndexMap.emplace_back(_backboneAtoms);
1058            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1059            proLINE = *(IndexMap[i].info->name);
1060            if( proLINE.compare("PRO") == 0 ){
1061                IndexMap[i].is_proline = true;
1062            }
1063
1064        }
1065        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
1066        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
1067        {
1068            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
1069        }
1070        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
1071        {
1072            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
1073        }
1074        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
1075        {
1076            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
1077        }
1078        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
1079        {
1080            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
1081            if (initParamz.addHydrogens == true){
1082                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1083            }
1084        }
1085        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
1086        {
1087            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1088        }
1089
1090
1091
1092 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
1093 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
1094 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
1095 //       }
1096    }
1097
1098    for (std::size_t j {1}; j < IndexMap.size(); ++j){
1099        IndexMap[j].prevResi = &(IndexMap[j - 1]);
1100
1101        IndexMap[j - 1].nextResi = &(IndexMap[j]);
1102
1103 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
1104 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
1105 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
1106 //         std::cout << IndexMap[j].prevResi->info->nr;
1107 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
1108 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
1109 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
1110 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
1111 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
1112 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
1113    }
1114
1115    nres = i + 1;
1116 }
1117
1118 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
1119 {
1120
1121     switch(initParams.NBS){
1122     case (NBSearchMethod::Classique): {
1123
1124         // store positions of CA atoms to use them for nbSearch
1125         std::vector<gmx::RVec> positionsCA_;
1126         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
1127         {
1128             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
1129         }
1130
1131         AnalysisNeighborhood nb_;
1132         nb_.setCutoff(initParams.cutoff_);
1133         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
1134         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
1135         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
1136         gmx::AnalysisNeighborhoodPair       pair;
1137         while (pairSearch.findNextPair(&pair))
1138         {
1139             if(CalculateAtomicDistances(
1140                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1141                 < minimalCAdistance){
1142                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
1143                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
1144                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
1145                 }
1146             }
1147         }
1148
1149         break;
1150     }
1151     case (NBSearchMethod::Experimental): { // TODO FIX
1152
1153         alternateNeighborhoodSearch as_;
1154
1155         as_.setCutoff(initParams.cutoff_);
1156
1157         as_.AltPairSearch(fr, IndexMap);
1158
1159         while (as_.findNextPair()){
1160             if(CalculateAtomicDistances(
1161                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1162                 < minimalCAdistance){
1163                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
1164                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
1165                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
1166                 }
1167             }
1168         }
1169
1170         break;
1171     }
1172     default: {
1173
1174         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
1175             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
1176                 if(CalculateAtomicDistances(
1177                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1178                     < minimalCAdistance){
1179                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
1180                     if (Acceptor != Donor + 1){
1181                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
1182                     }
1183                 }
1184             }
1185         }
1186         break;
1187     }
1188     }
1189
1190
1191 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
1192 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
1193 //    }
1194
1195    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices, initParams.pp_stretch);
1196    calculateBends(fr, pbc);
1197    calculateDihedrals(fr, pbc);
1198    Storage.storageData(frnr, PatternSearch.patternSearch());
1199
1200 }
1201
1202 std::vector<std::pair<int, std::string>> DsspTool::getData(){
1203     return Storage.returnData();
1204 }
1205
1206 } // namespace analysismodules
1207
1208 } // namespace gmx