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