src/dssptools.cpp

   1 /*
   2 * This file is part of the GROMACS molecular simulation package.
   3 *
   4 * Copyright (c) 2021, by the GROMACS development team, led by
   5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 * and including many others, as listed in the AUTHORS file in the
   7 * top-level source directory and at http://www.gromacs.org.
   8 *
   9 * GROMACS is free software; you can redistribute it and/or
  10 * modify it under the terms of the GNU Lesser General Public License
  11 * as published by the Free Software Foundation; either version 2.1
  12 * of the License, or (at your option) any later version.
  13 *
  14 * GROMACS is distributed in the hope that it will be useful,
  15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17 * Lesser General Public License for more details.
  18 *
  19 * You should have received a copy of the GNU Lesser General Public
  20 * License along with GROMACS; if not, see
  21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23 *
  24 * If you want to redistribute modifications to GROMACS, please
  25 * consider that scientific software is very special. Version
  26 * control is crucial - bugs must be traceable. We will be happy to
  27 * consider code for inclusion in the official distribution, but
  28 * derived work must not be called official GROMACS. Details are found
  29 * in the README & COPYING files - if they are missing, get the
  30 * official version at http://www.gromacs.org.
  31 *
  32 * To help us fund GROMACS development, we humbly ask that you cite
  33 * the research papers on the package. Check out http://www.gromacs.org.
  34 */
  35 /*! \internal \file
  36 * \brief
  37 * Implements gmx::analysismodules::Trajectory.
  38 *
  39 * \author Sergey Gorelov <gorelov_sv@pnpi.nrcki.ru>
  40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
  41 * \author Alexey Shvetsov <alexxyum@gmail.com>
  42 * \ingroup module_trajectoryanalysis
  43 */
  44
  45 /*
  46     There's something wrong with energy calculations of redidues with E ≈ -0
  47 */
  48
  49
  50 #include "dssptools.h"
  51
  52 #include <algorithm>
  53 #include "gromacs/math/units.h"
  54
  55 #include "gromacs/pbcutil/pbc.h"
  56 #include <gromacs/trajectoryanalysis.h>
  57 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  58 #include <set>
  59 #include <fstream>
  60 #include <mutex>
  61 #include <iostream>
  62
  63 namespace gmx
  64 {
  65
  66 namespace analysismodules
  67 {
  68
  69 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
  70 //{
  71 //   _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
  72 //}
  73
  74 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
  75 //{
  76 //   return _ResInfo[static_cast<std::size_t>(atomTypeName)];
  77 //}
  78
  79 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
  80     return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
  81 }
  82
  83 secondaryStructures::secondaryStructures(){
  84 }
  85 void secondaryStructures::initiateSearch(const std::vector<ResInfo> &ResInfoMatrix, const bool PiHelicesPreferencez, 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{}, vBD{}, 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[D], fr.x[B], vBD.as_vec());
 747
 748     for(std::size_t i{XX}, j{j + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
 749         if (j > 2){
 750             j -= 3;
 751         }
 752         if (k > 2){
 753             k -= 3;
 754         }
 755         p[i] = (vBD[j] * vBA[k]) - (vBD[k] * vBA[j]);
 756         x[i] = (vBD[j] * vDC[k]) - (vBD[k] * vDC[j]);
 757
 758     }
 759     for(std::size_t i{XX}, j{j + 1}, k{i + 2}; i <= ZZ; ++i, ++j, ++k){
 760         if (j > 2){
 761             j -= 3;
 762         }
 763         if (k > 2){
 764             k -= 3;
 765         }
 766         y[i] = (vBD[j] * x[k]) - (vBD[k] * x[j]);
 767     }
 768
 769     u = (x[XX] * x[XX]) + (x[YY] * x[YY]) + (x[ZZ] * x[ZZ]);
 770     v = (y[XX] * y[XX]) + (y[YY] * y[YY]) + (y[ZZ] * y[ZZ]);
 771
 772     if (u > 0 and v > 0){
 773         u = ((p[XX] * x[XX]) + (p[YY] * x[YY]) + (p[ZZ] * x[ZZ])) / std::sqrt(u);
 774         v = ((p[XX] * y[XX]) + (p[YY] * y[YY]) + (p[ZZ] * y[ZZ])) / std::sqrt(v);
 775         if (u != 0 or v != 0){
 776             result = std::atan2(v, u) * gmx::c_rad2Deg;
 777         }
 778     }
 779     return result;
 780 }
 781
 782 void DsspTool::calculateDihedrals(const t_trxframe &fr, const t_pbc *pbc){
 783     const float epsilon = 29;
 784     const float phi_min = -75 - epsilon;
 785     const float phi_max = -75 + epsilon;
 786     const float psi_min = 145 - epsilon;
 787     const float psi_max = 145 + epsilon;
 788     std::vector<float>          phi, psi;
 789     phi.resize(0);
 790     psi.resize(0);
 791     phi.resize(IndexMap.size(), 360);
 792     psi.resize(IndexMap.size(), 360);
 793
 794     for (std::size_t i = 1; i + 1 < IndexMap.size(); ++i){ // TODO add index verifictaion (check if those atom indexes exist)
 795         phi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i - 1].getIndex(backboneAtomTypes::AtomC)),
 796                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
 797                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
 798                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 799                                         fr,
 800                                         pbc);
 801         psi[i] = CalculateDihedralAngle(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomN)),
 802                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomCA)),
 803                                         static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 804                                         static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 805                                         fr,
 806                                         pbc);
 807     }
 808
 809     for (std::size_t i = 1; i + 3 < IndexMap.size(); ++i){
 810         switch (initParams.pp_stretch){
 811         case 2: {
 812             if (phi_min > phi[i] or phi[i] > phi_max or
 813                 phi_min > phi[i + 1] or phi[i + 1]> phi_max){
 814                 continue;
 815             }
 816
 817             if (psi_min > psi[i] or psi[i] > psi_max or
 818                 psi_min > psi[i + 1] or psi[i + 1] > psi_max){
 819                 continue;
 820             }
 821
 822             switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
 823                 case HelixPositions::None:
 824                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
 825                     break;
 826
 827                 case HelixPositions::End:
 828                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
 829                     break;
 830
 831                 default:
 832                     break;
 833             }
 834
 835             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
 836             /* Пропустил проверку того, что заменяемая ак - петля */
 837             PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
 838             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
 839         break;
 840         }
 841         case 3:{
 842             if (phi_min > phi[i] or phi[i] > phi_max or
 843                 phi_min > phi[i + 1] or phi[i + 1]> phi_max or
 844                 phi_min > phi[i + 2] or phi[i + 2]> phi_max){
 845                 continue;
 846             }
 847
 848             if (psi_min > psi[i] or psi[i] > psi_max or
 849                 psi_min > psi[i + 1] or psi[i + 1] > psi_max or
 850                 psi_min > psi[i + 2] or psi[i + 2] > psi_max){
 851                 continue;
 852             }
 853
 854             switch (PatternSearch.SecondaryStructuresStatusMap[i].getStatus(turnsTypes::Turn_PP)){
 855                 case HelixPositions::None:
 856                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start, turnsTypes::Turn_PP);
 857                     break;
 858
 859                 case HelixPositions::End:
 860                     PatternSearch.SecondaryStructuresStatusMap[i].setStatus(HelixPositions::Start_AND_End, turnsTypes::Turn_PP);
 861                     break;
 862
 863                 default:
 864                     break;
 865             }
 866
 867             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(HelixPositions::Middle, turnsTypes::Turn_PP);
 868             PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(HelixPositions::End, turnsTypes::Turn_PP);
 869             /* Пропустил проверку того, что заменяемая ак - петля */
 870             PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Helix_PP);
 871             PatternSearch.SecondaryStructuresStatusMap[i + 1].setStatus(secondaryStructureTypes::Helix_PP);
 872             PatternSearch.SecondaryStructuresStatusMap[i + 2].setStatus(secondaryStructureTypes::Helix_PP);
 873
 874             break;
 875         }
 876         default:
 877             throw std::runtime_error("Unsupported stretch length");
 878         }
 879     }
 880
 881 }
 882
 883 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 884                        ResInfo& Acceptor,
 885                        const t_trxframe&          fr,
 886                        const t_pbc*               pbc)
 887 {
 888    /*
 889     * DSSP uses eq from dssp 2.x
 890     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 891     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 892     * if R is in A
 893     * Hbond if E < -0.5
 894     *
 895     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 896     *
 897     */
 898
 899     if (CalculateAtomicDistances(
 900                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 901         >= minimalCAdistance)
 902     {
 903         return void();
 904     }
 905
 906     const float kCouplingConstant = 27.888;
 907     const float minimalAtomDistance{ 0.5 },
 908             minEnergy{ -9.9 };
 909     float HbondEnergy{ 0 };
 910     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 911
 912 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 913
 914     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 915                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 916         distanceNO = CalculateAtomicDistances(
 917                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 918         distanceNC = CalculateAtomicDistances(
 919                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 920         if (initParams.addHydrogens){
 921             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 922                rvec atomH{};
 923                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 924                for (int i{XX}; i <= ZZ; ++i){
 925                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 926                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 927                    atomH[i] += prevCO / prevCODist;
 928                }
 929                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 930                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 931             }
 932             else{
 933                 distanceHO = distanceNO;
 934                 distanceHC = distanceNC;
 935             }
 936        }
 937        else {
 938            distanceHO = CalculateAtomicDistances(
 939                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 940            distanceHC = CalculateAtomicDistances(
 941                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 942        }
 943        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 944         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 945        {
 946             HbondEnergy = minEnergy;
 947        }
 948        else{
 949            HbondEnergy =
 950                    kCouplingConstant
 951                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 952        }
 953
 954 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 955 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 956 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 957 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 958 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 959 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 960
 961        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 962
 963 //       if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
 964 //            HbondEnergy = minEnergy;
 965 //       }
 966
 967 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 968     }
 969 //    else{
 970 //        std::cout << "Donor Is Proline" << std::endl;
 971 //    }
 972
 973     if (HbondEnergy < Donor.acceptorEnergy[0]){
 974            Donor.acceptor[1] = Donor.acceptor[0];
 975            Donor.acceptor[0] = Acceptor.info;
 976            Donor.acceptorEnergy[0] = HbondEnergy;
 977     }
 978     else if (HbondEnergy < Donor.acceptorEnergy[1]){
 979            Donor.acceptor[1] = Acceptor.info;
 980            Donor.acceptorEnergy[1] = HbondEnergy;
 981     }
 982
 983     if (HbondEnergy < Acceptor.donorEnergy[0]){
 984            Acceptor.donor[1] = Acceptor.donor[0];
 985            Acceptor.donor[0] = Donor.info;
 986            Acceptor.donorEnergy[0] = HbondEnergy;
 987     }
 988     else if (HbondEnergy < Acceptor.donorEnergy[1]){
 989            Acceptor.donor[1] = Donor.info;
 990            Acceptor.donorEnergy[1] = HbondEnergy;
 991     }
 992 }
 993
 994
 995 /* Calculate Distance From B to A */
 996 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 997 {
 998    gmx::RVec r{ 0, 0, 0 };
 999    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
1000    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1001 }
1002
1003 /* Calculate Distance From B to A, where A is only fake coordinates */
1004 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
1005 {
1006    gmx::RVec r{ 0, 0, 0 };
1007    pbc_dx(pbc, A, fr.x[B], r.as_vec());
1008    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
1009 }
1010
1011 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
1012 {
1013    initParams = initParamz;
1014    ResInfo _backboneAtoms;
1015    std::size_t                 i{ 0 };
1016    std::string proLINE;
1017    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
1018    IndexMap.resize(0);
1019    IndexMap.push_back(_backboneAtoms);
1020    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1021    proLINE = *(IndexMap[i].info->name);
1022    if( proLINE.compare("PRO") == 0 ){
1023        IndexMap[i].is_proline = true;
1024    }
1025
1026    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
1027        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
1028        {
1029            ++i;
1030            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
1031            IndexMap.emplace_back(_backboneAtoms);
1032            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
1033            proLINE = *(IndexMap[i].info->name);
1034            if( proLINE.compare("PRO") == 0 ){
1035                IndexMap[i].is_proline = true;
1036            }
1037
1038        }
1039        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
1040        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
1041        {
1042            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
1043        }
1044        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
1045        {
1046            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
1047        }
1048        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
1049        {
1050            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
1051        }
1052        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
1053        {
1054            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
1055            if (initParamz.addHydrogens == true){
1056                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1057            }
1058        }
1059        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
1060        {
1061            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
1062        }
1063
1064
1065
1066 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
1067 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
1068 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
1069 //       }
1070    }
1071
1072    for (std::size_t j {1}; j < IndexMap.size(); ++j){
1073        IndexMap[j].prevResi = &(IndexMap[j - 1]);
1074
1075        IndexMap[j - 1].nextResi = &(IndexMap[j]);
1076
1077 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
1078 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
1079 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
1080 //         std::cout << IndexMap[j].prevResi->info->nr;
1081 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
1082 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
1083 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
1084 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
1085 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
1086 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
1087    }
1088
1089    nres = i + 1;
1090 }
1091
1092 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
1093 {
1094
1095     switch(initParams.NBS){
1096     case (NBSearchMethod::Classique): {
1097
1098         // store positions of CA atoms to use them for nbSearch
1099         std::vector<gmx::RVec> positionsCA_;
1100         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
1101         {
1102             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
1103         }
1104
1105         AnalysisNeighborhood nb_;
1106         nb_.setCutoff(initParams.cutoff_);
1107         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
1108         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
1109         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
1110         gmx::AnalysisNeighborhoodPair       pair;
1111         while (pairSearch.findNextPair(&pair))
1112         {
1113             if(CalculateAtomicDistances(
1114                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1115                 < minimalCAdistance){
1116                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
1117                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
1118                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
1119                 }
1120             }
1121         }
1122
1123         break;
1124     }
1125     case (NBSearchMethod::Experimental): { // TODO FIX
1126
1127         alternateNeighborhoodSearch as_;
1128
1129         as_.setCutoff(initParams.cutoff_);
1130
1131         as_.AltPairSearch(fr, IndexMap);
1132
1133         while (as_.findNextPair()){
1134             if(CalculateAtomicDistances(
1135                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1136                 < minimalCAdistance){
1137                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
1138                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
1139                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
1140                 }
1141             }
1142         }
1143
1144         break;
1145     }
1146     default: {
1147
1148         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
1149             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
1150                 if(CalculateAtomicDistances(
1151                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
1152                     < minimalCAdistance){
1153                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
1154                     if (Acceptor != Donor + 1){
1155                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
1156                     }
1157                 }
1158             }
1159         }
1160         break;
1161     }
1162     }
1163
1164
1165 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
1166 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
1167 //    }
1168
1169    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices, initParams.pp_stretch);
1170    calculateBends(fr, pbc);
1171    calculateDihedrals(fr, pbc);
1172    Storage.storageData(frnr, PatternSearch.patternSearch());
1173
1174 }
1175
1176 std::vector<std::pair<int, std::string>> DsspTool::getData(){
1177     return Storage.returnData();
1178 }
1179
1180 } // namespace analysismodules
1181
1182 } // namespace gmx