src/dssptools.cpp

   1 /*
   2 * This file is part of the GROMACS molecular simulation package.
   3 *
   4 * Copyright (c) 2021, by the GROMACS development team, led by
   5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 * and including many others, as listed in the AUTHORS file in the
   7 * top-level source directory and at http://www.gromacs.org.
   8 *
   9 * GROMACS is free software; you can redistribute it and/or
  10 * modify it under the terms of the GNU Lesser General Public License
  11 * as published by the Free Software Foundation; either version 2.1
  12 * of the License, or (at your option) any later version.
  13 *
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  17 * Lesser General Public License for more details.
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  34 */
  35 /*! \internal \file
  36 * \brief
  37 * Implements gmx::analysismodules::Trajectory.
  38 *
  39 * \author Sergey Gorelov <gorelov_sv@pnpi.nrcki.ru>
  40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
  41 * \author Alexey Shvetsov <alexxyum@gmail.com>
  42 * \ingroup module_trajectoryanalysis
  43 */
  44
  45 /*
  46     There's something wrong with energy 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, const int _pp_stretch){
  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     pp_stretch = _pp_stretch;
  92     SecondaryStructuresStatusMap.resize(ResInfoMatrix.size());
  93     SecondaryStructuresStringLine.resize(ResInfoMatrix.size(), '~');
  94 }
  95
  96 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName, bool status){
  97     SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = status;
  98     if (status){
  99         SecondaryStructuresStatus = secondaryStructureTypeName;
 100     }
 101     else{
 102         SecondaryStructuresStatus = secondaryStructureTypes::Loop;
 103     }
 104 }
 105
 106 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
 107     TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
 108 }
 109
 110 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
 111     return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
 112 }
 113
 114 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
 115     return breakPartners[0] == partner || breakPartners[1] == partner;
 116 }
 117
 118 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
 119     return TurnsStatusArray[static_cast<std::size_t>(turn)];
 120 }
 121
 122 secondaryStructureTypes secondaryStructures::secondaryStructuresData::getStatus() const{
 123     return  SecondaryStructuresStatus;
 124 }
 125
 126 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
 127     if (breakPartners[0] == nullptr){
 128         breakPartners[0] = breakPartner;
 129     }
 130     else{
 131         breakPartners[1] = breakPartner;
 132     }
 133     setStatus(secondaryStructureTypes::Break);
 134 }
 135
 136 void secondaryStructures::secondaryStructuresData::setBridge(secondaryStructuresData *bridgePartner, std::size_t bridgePartnerIndex, bridgeTypes bridgeType){
 137     if(bridgeType == bridgeTypes::ParallelBridge){
 138         bridgePartners[0] = bridgePartner;
 139         bridgePartnersIndexes[0] = bridgePartnerIndex;
 140     }
 141     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 142         bridgePartners[1] = bridgePartner;
 143         bridgePartnersIndexes[1] = bridgePartnerIndex;
 144     }
 145 }
 146
 147 bool secondaryStructures::secondaryStructuresData::hasBridges() const{
 148     return bridgePartners[0] || bridgePartners[1];
 149
 150 }
 151
 152 bool secondaryStructures::secondaryStructuresData::hasBridges(bridgeTypes bridgeType) const{
 153     if(bridgeType == bridgeTypes::ParallelBridge){
 154         return bridgePartners[0] != nullptr;
 155     }
 156     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 157         return bridgePartners[1] != nullptr;
 158     }
 159
 160     return false;
 161
 162 }
 163
 164 bool secondaryStructures::secondaryStructuresData::isBridgePartnerWith(secondaryStructuresData *bridgePartner, bridgeTypes bridgeType) const{
 165     if(bridgeType == bridgeTypes::ParallelBridge){
 166         return bridgePartners[0] == bridgePartner;
 167     }
 168     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 169         return bridgePartners[1] == bridgePartner;
 170     }
 171     return false;
 172 }
 173
 174 std::size_t secondaryStructures::secondaryStructuresData::getBridgePartnerIndex(bridgeTypes bridgeType) const{
 175     if (bridgeType == bridgeTypes::ParallelBridge){
 176         return bridgePartnersIndexes[0];
 177     }
 178     return bridgePartnersIndexes[1];
 179 }
 180
 181 secondaryStructures::secondaryStructuresData secondaryStructures::secondaryStructuresData::getBridgePartner(bridgeTypes bridgeType) const{
 182     if(bridgeType == bridgeTypes::ParallelBridge){
 183         return *(bridgePartners[0]);
 184     }
 185     return *(bridgePartners[1]);
 186 }
 187
 188 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
 189     if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
 190         (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
 191         (*ResInfoMap)[Acceptor].info == nullptr ){
 192 //        std::cout << "Bad hbond check. Reason(s): " ;
 193 //        if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 194 //            std::cout << "Donor has no acceptor[0]; ";
 195 //        }
 196 //        if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 197 //            std::cout << "Donor has no acceptor[1]; ";
 198 //        }
 199 //        if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 200 //            std::cout << "No info about acceptor; ";
 201 //        }
 202 //        std::cout << std::endl;
 203         return false;
 204     }
 205 //    else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
 206 //              (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
 207 //              (*ResInfoMap)[Donor].info == nullptr )) {
 208 //        std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
 209 //        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;
 210 //        std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
 211 //        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;
 212 //        std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
 213 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 214 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 215 //            std::cout << "HBond Exist" << std::endl;
 216 //        }
 217 //    }
 218 //    else {
 219 //        std::cout << "Bad hbond check. Reason(s): " ;
 220 //        if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
 221 //            std::cout << "Acceptor has no donor[0]; ";
 222 //        }
 223 //        if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
 224 //            std::cout << "Acceptor has no donor[1]; ";
 225 //        }
 226 //        if ( (*ResInfoMap)[Donor].info == nullptr ){
 227 //            std::cout << "No info about donor; ";
 228 //        }
 229 //        std::cout << std::endl;
 230 //    }
 231
 232     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 233            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 234
 235
 236 }
 237
 238 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 239     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 240     if ( i > j ){
 241         std::swap(i, j);
 242     }
 243
 244     for (; i != j; ++i){
 245         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 246 //            std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 247             return false;
 248         }
 249     }
 250     return true;
 251 }
 252
 253 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 254     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){ // Protection from idiotz, не обязательно нужен
 255         return bridgeTypes::None;
 256     }
 257
 258     ResInfo a{(*ResInfoMap)[i]}, b{(*ResInfoMap)[j]};
 259
 260     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1) && a.prevResi && a.nextResi && b.prevResi && b.nextResi){
 261         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){
 262             return bridgeTypes::ParallelBridge;
 263         }
 264         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){
 265             return bridgeTypes::AntiParallelBridge;
 266         }
 267     }
 268     return bridgeTypes::None;
 269 }
 270
 271 void secondaryStructures::analyzeBridgesAndStrandsPatterns(){
 272 //  Calculate Bridgez
 273     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 274         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 275             switch(calculateBridge(i, j)){
 276             case bridgeTypes::ParallelBridge : {
 277                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::ParallelBridge);
 278                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 279                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::ParallelBridge);
 280                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 281             }
 282             case bridgeTypes::AntiParallelBridge : {
 283                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), j, bridgeTypes::AntiParallelBridge);
 284                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 285                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), i, bridgeTypes::AntiParallelBridge);
 286                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 287             }
 288             default :
 289                 continue;
 290             }
 291         }
 292     }
 293 //  Calculate Extended Strandz
 294     for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 295         bool is_Estrand {false};
 296         for(std::size_t j {2}; j != 0; --j){
 297             for(const bridgeTypes &bridgeType : {bridgeTypes::ParallelBridge, bridgeTypes::AntiParallelBridge}){
 298                 if (SecondaryStructuresStatusMap[i].hasBridges(bridgeType) && SecondaryStructuresStatusMap[i + j].hasBridges(bridgeType) ){
 299                     std::size_t i_partner{SecondaryStructuresStatusMap[i].getBridgePartnerIndex(bridgeType)}, j_partner{SecondaryStructuresStatusMap[i + j].getBridgePartnerIndex(bridgeType)}, second_strand{};
 300                     if ( abs(i_partner - j_partner) < 6){
 301                         if (i_partner < j_partner){
 302                             second_strand = i_partner;
 303                         }
 304                         else{
 305                             second_strand = j_partner;
 306                         }
 307                         for(int k{abs(i_partner - j_partner)}; k >= 0; --k){
 308                             if (SecondaryStructuresStatusMap[second_strand + k].getStatus(secondaryStructureTypes::Bridge)){
 309                                 SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Bridge, false);
 310                             }
 311
 312                             SecondaryStructuresStatusMap[second_strand + k].setStatus(secondaryStructureTypes::Strand);
 313                         }
 314                         is_Estrand = true;
 315                     }
 316                 }
 317             }
 318             if (is_Estrand){
 319                 for(std::size_t k{0}; k <= j; ++k){
 320                     if (SecondaryStructuresStatusMap[i + k].getStatus(secondaryStructureTypes::Bridge)){
 321                         SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Bridge, false);
 322                     }
 323                     SecondaryStructuresStatusMap[i + k].setStatus(secondaryStructureTypes::Strand);
 324                 }
 325                 break;
 326             }
 327         }
 328     }
 329
 330
 331
 332
 333
 334
 335
 336
 337
 338
 339
 340
 341 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 342 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 343 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 344 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 345 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 346 //                    Bridge[i].push_back(j);
 347 //                }
 348 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 349 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 350 //                    AntiBridge[i].push_back(j);
 351 //                }
 352 //            }
 353 //        }
 354 //    }
 355 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 356 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 357 //            setStatus(i, secondaryStructureTypes::Bulge);
 358 //        }
 359 //    }
 360 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 361 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 362 //            if (j == i){
 363 //                continue;
 364 //            }
 365 //            else {
 366 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 367 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 368 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 369 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 370 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 371 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 372 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 373 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 374 //                                        < 5)){
 375 //                                    if (j < i){
 376 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 377 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 378 //                                        }
 379 //                                    }
 380 //                                    else{
 381 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 382 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 383 //                                        }
 384 //                                    }
 385 //                                }
 386 //                            }
 387 //                        }
 388 //                    }
 389 //                }
 390 //            }
 391 //        }
 392 //    }
 393 }
 394
 395 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 396     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 397         std::size_t stride {static_cast<std::size_t>(i) + 3};
 398         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 399             if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
 400                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 401
 402                 for (std::size_t k {1}; k < stride; ++k){
 403                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 404                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 405                         SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 406                     }
 407                 }
 408
 409                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 410                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 411                 }
 412                 else {
 413                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 414                 }
 415             }
 416         }
 417     }
 418
 419     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 420         std::size_t stride {static_cast<std::size_t>(i) + 3};
 421         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 422             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 423                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 424                 bool empty = true;
 425                 secondaryStructureTypes Helix;
 426                 switch(i){
 427                 case turnsTypes::Turn_3:
 428                     for (std::size_t k {0}; empty && k < stride; ++k){
 429                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 430                     }
 431                     Helix = secondaryStructureTypes::Helix_3;
 432                     break;
 433                 case turnsTypes::Turn_5:
 434                     for (std::size_t k {0}; empty && k < stride; ++k){
 435                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 436                     }
 437                     Helix = secondaryStructureTypes::Helix_5;
 438                     break;
 439                 default:
 440                     Helix = secondaryStructureTypes::Helix_4;
 441                     break;
 442                 }
 443                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 444                     for(std::size_t k {0}; k < stride; ++k ){
 445                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 446                     }
 447                 }
 448             }
 449         }
 450     }
 451
 452     /* Не знаю зач они в дссп так сделали, этож полное говно */
 453
 454 //    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 455 //        if (SecondaryStructuresStatusMap[i].getStatus() == secondaryStructureTypes::Loop || SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 456 //            bool isTurn = false;
 457 //            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 458 //                std::size_t stride {static_cast<std::size_t>(j) + 3};
 459 //                for(std::size_t k {1}; k < stride and !isTurn; ++k){
 460 //                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 461 //                }
 462 //            }
 463 //            if (isTurn){
 464 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 465 //            }
 466 //        }
 467 //    }
 468
 469 }
 470
 471 std::string secondaryStructures::patternSearch(){
 472
 473
 474     analyzeBridgesAndStrandsPatterns();
 475     analyzeTurnsAndHelicesPatterns();
 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 float DsspTool::CalculateDihedralAngle(const int &A, const int &B, const int &C, const int &D, const t_trxframe &fr, const t_pbc *pbc){
 742     float result{360}, u{}, v{};
 743     gmx::RVec vBA{}, vDC{}, vBC{}, p{}, x{}, y{};
 744     pbc_dx(pbc, fr.x[A], fr.x[B], vBA.as_vec());
 745     pbc_dx(pbc, fr.x[C], fr.x[D], vDC.as_vec());
 746     pbc_dx(pbc, fr.x[C], fr.x[B], vBC.as_vec());
 747
 748     for(auto &i : {vBA, vDC, vBC}){
 749         for(std::size_t j {XX}; j <= ZZ; ++j){
 750             i[j] *= gmx::c_nm2A;
 751         }
 752     }
 753
 754     for(std::size_t i{XX}, j{j + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
 755         if (j > 2){
 756             j -= 3;
 757         }
 758         if (k > 2){
 759             k -= 3;
 760         }
 761         p[i] = (vBC[j] * vBA[k]) - (vBC[k] * vBA[j]);
 762         x[i] = (vBC[j] * vDC[k]) - (vBC[k] * vDC[j]);
 763
 764     }
 765     for(std::size_t i{XX}, j{j + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
 766         if (j > 2){
 767             j -= 3;
 768         }
 769         if (k > 2){
 770             k -= 3;
 771         }
 772         y[i] = (vBC[j] * x[k]) - (vBC[k] * x[j]);
 773     }
 774
 775     std::cout << "v12 = " << vBA[0] << ", " << vBA[1] << ", " << vBA[2] << std::endl;
 776     std::cout << "v43 = " << vDC[0] << ", " << vDC[1] << ", " << vDC[2] << std::endl;
 777     std::cout << "z = " << vBC[0] << ", " << vBC[1] << ", " << vBC[2] << std::endl;
 778     std::cout << "p = " << p[0] << ", " << p[1] << ", " << p[2] << std::endl;
 779     std::cout << "x = " << x[0] << ", " << x[1] << ", " << x[2] << std::endl;
 780     std::cout << "y = " << y[0] << ", " << y[1] << ", " << y[2] << std::endl;
 781
 782     u = (x[XX] * x[XX]) + (x[YY] * x[YY]) + (x[ZZ] * x[ZZ]);
 783     v = (y[XX] * y[XX]) + (y[YY] * y[YY]) + (y[ZZ] * y[ZZ]);
 784
 785     std::cout << "u = " << u << std::endl;
 786     std::cout << "v = " << v << std::endl;
 787
 788     if (u > 0 and v > 0){
 789         u = ((p[XX] * x[XX]) + (p[YY] * x[YY]) + (p[ZZ] * x[ZZ])) / std::sqrt(u);
 790         v = ((p[XX] * y[XX]) + (p[YY] * y[YY]) + (p[ZZ] * y[ZZ])) / std::sqrt(v);
 791         std::cout << "new u = " << u << std::endl;
 792         std::cout << "new v = " << v << std::endl;
 793         if (u != 0 or v != 0){
 794             result = std::atan2(v, u) * gmx::c_rad2Deg;
 795         }
 796     }
 797     return result;
 798 }
 799
 800 void DsspTool::calculateDihedrals(const t_trxframe &fr, const t_pbc *pbc){
 801     const float epsilon = 29;
 802     const float phi_min = -75 - epsilon; // -104
 803     const float phi_max = -75 + epsilon; // -46
 804     const float psi_min = 145 - epsilon; // 116
 805     const float psi_max = 145 + epsilon; // 176
 806     std::vector<float>          phi(IndexMap.size(), 360), psi(IndexMap.size(), 360);
 807 //    phi.resize(0);
 808 //    psi.resize(0);
 809 //    phi.resize(IndexMap.size(), 360);
 810 //    psi.resize(IndexMap.size(), 360);
 811
 812     for (std::size_t i = 1; i + 1 < IndexMap.size(); ++i){ // TODO add index verifictaion (check if those atom indexes exist)
 813         std::cout << "For resi " << i << " :" << std::endl;
 814         phi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i - 1].getIndex(backboneAtomTypes::AtomC)),
 815                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
 816                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
 817                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 818                                         fr,
 819                                         pbc);
 820         psi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
 821                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
 822                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 823                                         static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 824                                         fr,
 825                                         pbc);
 826 //        std::cout << "For " << i << " phi = " << phi[i] << ", psi = " << psi[i] << std::endl;
 827         std::cout << "phi[" << i << "] = " << phi[i] << std::endl;
 828         std::cout << "psi[" << i << "] = " << psi[i] << std::endl;
 829     }
 830
 831     for (std::size_t i = 1; i + 3 < IndexMap.size(); ++i){
 832         switch (initParams.pp_stretch){
 833         case 2: {
 834             if (phi_min > phi[i] or phi[i] > phi_max or
 835                 phi_min > phi[i + 1] or phi[i + 1]> phi_max){
 836                 continue;
 837             }
 838
 839             if (psi_min > psi[i] or psi[i] > psi_max or
 840                 psi_min > psi[i + 1] or psi[i + 1] > psi_max){
 841                 continue;
 842             }
 843
 844             switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
 845                 case HelixPositions::None:
 846                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
 847                     break;
 848
 849                 case HelixPositions::End:
 850                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
 851                     break;
 852
 853                 default:
 854                     break;
 855             }
 856
 857             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
 858             /* Пропустил проверку того, что заменяемая ак - петля */
 859             PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
 860             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
 861             break;
 862         }
 863         case 3:{
 864             if (phi_min > phi[i] or phi[i] > phi_max or
 865                 phi_min > phi[i + 1] or phi[i + 1]> phi_max or
 866                 phi_min > phi[i + 2] or phi[i + 2]> phi_max){
 867                 continue;
 868             }
 869
 870             if (psi_min > psi[i] or psi[i] > psi_max or
 871                 psi_min > psi[i + 1] or psi[i + 1] > psi_max or
 872                 psi_min > psi[i + 2] or psi[i + 2] > psi_max){
 873                 continue;
 874             }
 875
 876             switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
 877                 case HelixPositions::None:
 878                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
 879                     break;
 880
 881                 case HelixPositions::End:
 882                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
 883                     break;
 884
 885                 default:
 886                     break;
 887             }
 888
 889             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::Middle, turnsTypes::Turn_PP);
 890             PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
 891             /* Пропустил проверку того, что заменяемая ак - петля */
 892             PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
 893             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
 894             PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(secondaryStructureTypes::Helix_PP);
 895
 896             break;
 897         }
 898         default:
 899             throw std::runtime_error("Unsupported stretch length");
 900         }
 901     }
 902
 903 }
 904
 905 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 906                        ResInfo& Acceptor,
 907                        const t_trxframe&          fr,
 908                        const t_pbc*               pbc)
 909 {
 910    /*
 911     * DSSP uses eq from dssp 2.x
 912     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 913     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 914     * if R is in A
 915     * Hbond if E < -0.5
 916     *
 917     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 918     *
 919     */
 920
 921     if (CalculateAtomicDistances(
 922                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 923         >= minimalCAdistance)
 924     {
 925         return void();
 926     }
 927
 928     const float kCouplingConstant = 27.888;
 929     const float minimalAtomDistance{ 0.5 },
 930             minEnergy{ -9.9 };
 931     float HbondEnergy{ 0 };
 932     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 933
 934 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 935
 936     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 937                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 938         distanceNO = CalculateAtomicDistances(
 939                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 940         distanceNC = CalculateAtomicDistances(
 941                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 942         if (initParams.addHydrogens){
 943             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 944                rvec atomH{};
 945                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 946                for (int i{XX}; i <= ZZ; ++i){
 947                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 948                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 949                    atomH[i] += prevCO / prevCODist;
 950                }
 951                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 952                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 953             }
 954             else{
 955                 distanceHO = distanceNO;
 956                 distanceHC = distanceNC;
 957             }
 958        }
 959        else {
 960            distanceHO = CalculateAtomicDistances(
 961                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 962            distanceHC = CalculateAtomicDistances(
 963                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 964        }
 965        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 966         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 967        {
 968             HbondEnergy = minEnergy;
 969        }
 970        else{
 971            HbondEnergy =
 972                    kCouplingConstant
 973                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 974        }
 975
 976 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 977 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 978 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 979 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 980 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 981 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 982
 983        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 984
 985 //       if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
 986 //            HbondEnergy = minEnergy;
 987 //       }
 988
 989 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 990     }
 991 //    else{
 992 //        std::cout << "Donor Is Proline" << std::endl;
 993 //    }
 994
 995     if (HbondEnergy < Donor.acceptorEnergy[0]){
 996            Donor.acceptor[1] = Donor.acceptor[0];
 997            Donor.acceptor[0] = Acceptor.info;
 998            Donor.acceptorEnergy[0] = HbondEnergy;
 999     }
1000     else if (HbondEnergy < Donor.acceptorEnergy[1]){
1001            Donor.acceptor[1] = Acceptor.info;
1002            Donor.acceptorEnergy[1] = HbondEnergy;
1003     }
1004
1005     if (HbondEnergy < Acceptor.donorEnergy[0]){
1006            Acceptor.donor[1] = Acceptor.donor[0];
1007            Acceptor.donor[0] = Donor.info;
1008            Acceptor.donorEnergy[0] = HbondEnergy;
1009     }
1010     else if (HbondEnergy < Acceptor.donorEnergy[1]){
1011            Acceptor.donor[1] = Donor.info;
1012            Acceptor.donorEnergy[1] = HbondEnergy;
1013     }
1014 }
1015
1016
1017 /* Calculate Distance From B to A */
1018 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1019 {
1020    gmx::RVec r{ 0, 0, 0 };
1021    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
1022    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1023 }
1024
1025 /* Calculate Distance From B to A, where A is only fake coordinates */
1026 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1027 {
1028    gmx::RVec r{ 0, 0, 0 };
1029    pbc_dx(pbc, A, fr.x[B], r.as_vec());
1030    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1031 }
1032
1033 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
1034 {
1035    initParams = initParamz;
1036    ResInfo _backboneAtoms;
1037    std::size_t                 i{ 0 };
1038    std::string proLINE;
1039    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
1040    IndexMap.resize(0);
1041    IndexMap.push_back(_backboneAtoms);
1042    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1043    proLINE = *(IndexMap[i].info->name);
1044    if( proLINE.compare("PRO") == 0 ){
1045        IndexMap[i].is_proline = true;
1046    }
1047
1048    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
1049        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
1050        {
1051            ++i;
1052            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
1053            IndexMap.emplace_back(_backboneAtoms);
1054            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1055            proLINE = *(IndexMap[i].info->name);
1056            if( proLINE.compare("PRO") == 0 ){
1057                IndexMap[i].is_proline = true;
1058            }
1059
1060        }
1061        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
1062        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
1063        {
1064            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
1065        }
1066        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
1067        {
1068            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
1069        }
1070        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
1071        {
1072            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
1073        }
1074        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
1075        {
1076            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
1077            if (initParamz.addHydrogens == true){
1078                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1079            }
1080        }
1081        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
1082        {
1083            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1084        }
1085
1086
1087
1088 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
1089 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
1090 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
1091 //       }
1092    }
1093
1094    for (std::size_t j {1}; j < IndexMap.size(); ++j){
1095        IndexMap[j].prevResi = &(IndexMap[j - 1]);
1096
1097        IndexMap[j - 1].nextResi = &(IndexMap[j]);
1098
1099 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
1100 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
1101 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
1102 //         std::cout << IndexMap[j].prevResi->info->nr;
1103 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
1104 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
1105 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
1106 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
1107 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
1108 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
1109    }
1110
1111    nres = i + 1;
1112 }
1113
1114 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
1115 {
1116
1117     switch(initParams.NBS){
1118     case (NBSearchMethod::Classique): {
1119
1120         // store positions of CA atoms to use them for nbSearch
1121         std::vector<gmx::RVec> positionsCA_;
1122         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
1123         {
1124             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
1125         }
1126
1127         AnalysisNeighborhood nb_;
1128         nb_.setCutoff(initParams.cutoff_);
1129         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
1130         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
1131         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
1132         gmx::AnalysisNeighborhoodPair       pair;
1133         while (pairSearch.findNextPair(&pair))
1134         {
1135             if(CalculateAtomicDistances(
1136                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1137                 < minimalCAdistance){
1138                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
1139                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
1140                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
1141                 }
1142             }
1143         }
1144
1145         break;
1146     }
1147     case (NBSearchMethod::Experimental): { // TODO FIX
1148
1149         alternateNeighborhoodSearch as_;
1150
1151         as_.setCutoff(initParams.cutoff_);
1152
1153         as_.AltPairSearch(fr, IndexMap);
1154
1155         while (as_.findNextPair()){
1156             if(CalculateAtomicDistances(
1157                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1158                 < minimalCAdistance){
1159                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
1160                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
1161                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
1162                 }
1163             }
1164         }
1165
1166         break;
1167     }
1168     default: {
1169
1170         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
1171             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
1172                 if(CalculateAtomicDistances(
1173                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1174                     < minimalCAdistance){
1175                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
1176                     if (Acceptor != Donor + 1){
1177                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
1178                     }
1179                 }
1180             }
1181         }
1182         break;
1183     }
1184     }
1185
1186
1187 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
1188 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
1189 //    }
1190
1191    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices, initParams.pp_stretch);
1192    calculateBends(fr, pbc);
1193    calculateDihedrals(fr, pbc);
1194    Storage.storageData(frnr, PatternSearch.patternSearch());
1195
1196 }
1197
1198 std::vector<std::pair<int, std::string>> DsspTool::getData(){
1199     return Storage.returnData();
1200 }
1201
1202 } // namespace analysismodules
1203
1204 } // namespace gmx