src/dssptools.cpp

   1 /*
   2 * This file is part of the GROMACS molecular simulation package.
   3 *
   4 * Copyright (c) 2021, by the GROMACS development team, led by
   5 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6 * and including many others, as listed in the AUTHORS file in the
   7 * top-level source directory and at http://www.gromacs.org.
   8 *
   9 * GROMACS is free software; you can redistribute it and/or
  10 * modify it under the terms of the GNU Lesser General Public License
  11 * as published by the Free Software Foundation; either version 2.1
  12 * of the License, or (at your option) any later version.
  13 *
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  17 * Lesser General Public License for more details.
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  34 */
  35 /*! \internal \file
  36 * \brief
  37 * Implements gmx::analysismodules::Trajectory.
  38 *
  39 * \author Sergey Gorelov <gorelov_sv@pnpi.nrcki.ru>
  40 * \author Anatoly Titov <titov_ai@pnpi.nrcki.ru>
  41 * \author Alexey Shvetsov <alexxyum@gmail.com>
  42 * \ingroup module_trajectoryanalysis
  43 */
  44
  45 /*
  46     There's something wrong with energy calculations of redidues with E ≈ -0
  47 */
  48
  49
  50 #include "dssptools.h"
  51
  52 #include <algorithm>
  53 #include "gromacs/math/units.h"
  54
  55 #include "gromacs/pbcutil/pbc.h"
  56 #include <gromacs/trajectoryanalysis.h>
  57 #include "gromacs/trajectoryanalysis/topologyinformation.h"
  58 #include <set>
  59 #include <fstream>
  60 #include <mutex>
  61 #include <iostream>
  62
  63 namespace gmx
  64 {
  65
  66 namespace analysismodules
  67 {
  68
  69 //void ResInfo::setIndex(backboneAtomTypes atomTypeName, std::size_t atomIndex)
  70 //{
  71 //   _ResInfo.at(static_cast<std::size_t>(atomTypeName)) = atomIndex;
  72 //}
  73
  74 //std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const
  75 //{
  76 //   return _ResInfo[static_cast<std::size_t>(atomTypeName)];
  77 //}
  78
  79 std::size_t ResInfo::getIndex(backboneAtomTypes atomTypeName) const{
  80     return _backboneIndices[static_cast<std::size_t>(atomTypeName)];
  81 }
  82
  83 secondaryStructures::secondaryStructures(){
  84 }
  85 void secondaryStructures::initiateSearch(const std::vector<ResInfo> &ResInfoMatrix, const bool PiHelicesPreferencez){
  86     SecondaryStructuresStatusMap.resize(0);
  87     SecondaryStructuresStringLine.resize(0);
  88     std::vector<std::size_t> temp; temp.resize(0),
  89     PiHelixPreference = PiHelicesPreferencez;
  90     ResInfoMap = &ResInfoMatrix;
  91     SecondaryStructuresStatusMap.resize(ResInfoMatrix.size());
  92     SecondaryStructuresStringLine.resize(ResInfoMatrix.size(), '~');
  93 }
  94
  95 void secondaryStructures::secondaryStructuresData::setStatus(const secondaryStructureTypes secondaryStructureTypeName){
  96     SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)] = true;
  97     SecondaryStructuresStatus = secondaryStructureTypeName;
  98 }
  99
 100 void secondaryStructures::secondaryStructuresData::setStatus(const HelixPositions helixPosition, const turnsTypes turn){
 101     TurnsStatusArray[static_cast<std::size_t>(turn)] = helixPosition;
 102 }
 103
 104 bool secondaryStructures::secondaryStructuresData::getStatus(const secondaryStructureTypes secondaryStructureTypeName) const{
 105     return SecondaryStructuresStatusArray[static_cast<std::size_t>(secondaryStructureTypeName)];
 106 }
 107
 108 bool secondaryStructures::secondaryStructuresData::isBreakPartnerWith(const secondaryStructuresData *partner) const{
 109     return breakPartners[0] == partner || breakPartners[1] == partner;
 110 }
 111
 112 HelixPositions secondaryStructures::secondaryStructuresData::getStatus(const turnsTypes turn) const{
 113     return TurnsStatusArray[static_cast<std::size_t>(turn)];
 114 }
 115
 116 secondaryStructureTypes secondaryStructures::secondaryStructuresData::getStatus() const{
 117     return  SecondaryStructuresStatus;
 118 }
 119
 120 void secondaryStructures::secondaryStructuresData::setBreak(secondaryStructuresData *breakPartner){
 121     if (breakPartners[0] == nullptr){
 122         breakPartners[0] = breakPartner;
 123     }
 124     else{
 125         breakPartners[1] = breakPartner;
 126     }
 127     setStatus(secondaryStructureTypes::Break);
 128 }
 129
 130 void secondaryStructures::secondaryStructuresData::setBridge(secondaryStructuresData *bridgePartner, bridgeTypes bridgeType){
 131     if(bridgeType == bridgeTypes::ParallelBridge){
 132         bridgePartners[0] = bridgePartner;
 133     }
 134     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 135         bridgePartners[1] = bridgePartner;
 136     }
 137 }
 138
 139 bool secondaryStructures::secondaryStructuresData::hasBridges() const{
 140     return bridgePartners[0] || bridgePartners[1];
 141
 142 }
 143
 144 bool secondaryStructures::secondaryStructuresData::isBridgePartnerWith(secondaryStructuresData *bridgePartner, bridgeTypes bridgeType) const{
 145     if(bridgeType == bridgeTypes::ParallelBridge){
 146         return bridgePartners[0] == bridgePartner;
 147     }
 148     else if (bridgeType == bridgeTypes::AntiParallelBridge){
 149         return bridgePartners[1] == bridgePartner;
 150     }
 151     return false;
 152 }
 153
 154 bool secondaryStructures::hasHBondBetween(std::size_t Donor, std::size_t Acceptor) const{
 155     if( (*ResInfoMap)[Donor].acceptor[0] == nullptr ||
 156         (*ResInfoMap)[Donor].acceptor[1] == nullptr ||
 157         (*ResInfoMap)[Acceptor].info == nullptr ){
 158 //        std::cout << "Bad hbond check. Reason(s): " ;
 159 //        if ( (*ResInfoMap)[Donor].acceptor[0] == nullptr ){
 160 //            std::cout << "Donor has no acceptor[0]; ";
 161 //        }
 162 //        if ( (*ResInfoMap)[Donor].acceptor[1] == nullptr ){
 163 //            std::cout << "Donor has no acceptor[1]; ";
 164 //        }
 165 //        if ( (*ResInfoMap)[Acceptor].info == nullptr ){
 166 //            std::cout << "No info about acceptor; ";
 167 //        }
 168 //        std::cout << std::endl;
 169         return false;
 170     }
 171 //    else if (!( (*ResInfoMap)[Acceptor].donor[0] == nullptr ||
 172 //              (*ResInfoMap)[Acceptor].donor[1] == nullptr ||
 173 //              (*ResInfoMap)[Donor].info == nullptr )) {
 174 //        std::cout << "Comparing DONOR №" << (*ResInfoMap)[Donor].info->nr << " And ACCEPTOR №" << (*ResInfoMap)[Acceptor].info->nr << ": " << std::endl;
 175 //        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;
 176 //        std::cout << "Donor's acceptors' energy are = " << (*ResInfoMap)[Donor].acceptorEnergy[0] << ", " << (*ResInfoMap)[Donor].acceptorEnergy[1] << std::endl;
 177 //        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;
 178 //        std::cout << "Acceptors's donors' energy are = " << (*ResInfoMap)[Acceptor].donorEnergy[0] << ", " << (*ResInfoMap)[Acceptor].donorEnergy[1] << std::endl;
 179 //        if( ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 180 //                ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff ) ){
 181 //            std::cout << "HBond Exist" << std::endl;
 182 //        }
 183 //    }
 184 //    else {
 185 //        std::cout << "Bad hbond check. Reason(s): " ;
 186 //        if ( (*ResInfoMap)[Acceptor].donor[0] == nullptr ){
 187 //            std::cout << "Acceptor has no donor[0]; ";
 188 //        }
 189 //        if ( (*ResInfoMap)[Acceptor].donor[1] == nullptr ){
 190 //            std::cout << "Acceptor has no donor[1]; ";
 191 //        }
 192 //        if ( (*ResInfoMap)[Donor].info == nullptr ){
 193 //            std::cout << "No info about donor; ";
 194 //        }
 195 //        std::cout << std::endl;
 196 //    }
 197
 198     return ( (*ResInfoMap)[Donor].acceptor[0] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[0] < HBondEnergyCutOff ) ||
 199            ( (*ResInfoMap)[Donor].acceptor[1] == (*ResInfoMap)[Acceptor].info && (*ResInfoMap)[Donor].acceptorEnergy[1] < HBondEnergyCutOff );
 200
 201
 202 }
 203
 204 bool secondaryStructures::NoChainBreaksBetween(std::size_t Resi1, std::size_t Resi2) const{
 205     std::size_t i{Resi1}, j{Resi2}; // From i to j → i <= j
 206     if ( i > j ){
 207         std::swap(i, j);
 208     }
 209
 210     for (; i != j; ++i){
 211         if ( SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 212             std::cout << "Patternsearch has detected a CHAINBREAK between " << Resi1 << " and " << Resi2 << std::endl;
 213             return false;
 214         }
 215     }
 216     return true;
 217 }
 218
 219 bridgeTypes secondaryStructures::calculateBridge(std::size_t i, std::size_t j) const{
 220     if( i < 1 || j < 1 || i + 1 >= ResInfoMap->size() || j + 1 >= ResInfoMap->size() ){ // Protection from idiotz, не обязательно нужен
 221         return bridgeTypes::None;
 222     }
 223
 224     ResInfo a{(*ResInfoMap)[i]}, b{(*ResInfoMap)[j]};
 225
 226     if(NoChainBreaksBetween(i - 1, i + 1) && NoChainBreaksBetween(j - 1, j + 1) && a.prevResi && a.nextResi && b.prevResi && b.nextResi){
 227         if((hasHBondBetween(i + 1, j) && hasHBondBetween(j, i - 1)) || (hasHBondBetween(j + 1, i) && hasHBondBetween(i, j - 1)) ){
 228             return bridgeTypes::ParallelBridge;
 229         }
 230         else if((hasHBondBetween(i + 1, j - 1) && hasHBondBetween(j + 1, i - 1)) || (hasHBondBetween(j, i) && hasHBondBetween(i, j)) ){
 231             return bridgeTypes::AntiParallelBridge;
 232         }
 233     }
 234     return bridgeTypes::None;
 235 }
 236
 237 void secondaryStructures::analyzeBridgesAndLaddersPatterns(){
 238     for(std::size_t i {1}; i + 4 < SecondaryStructuresStatusMap.size(); ++i){
 239         for(std::size_t j {i + 3}; j + 1 < SecondaryStructuresStatusMap.size(); ++j ){
 240             switch(calculateBridge(i, j)){
 241             case bridgeTypes::ParallelBridge : {
 242                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), bridgeTypes::ParallelBridge);
 243                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 244                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), bridgeTypes::ParallelBridge);
 245                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 246             }
 247             case bridgeTypes::AntiParallelBridge : {
 248                 SecondaryStructuresStatusMap[i].setBridge(&(SecondaryStructuresStatusMap[j]), bridgeTypes::AntiParallelBridge);
 249                 SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bridge);
 250                 SecondaryStructuresStatusMap[j].setBridge(&(SecondaryStructuresStatusMap[i]), bridgeTypes::AntiParallelBridge);
 251                 SecondaryStructuresStatusMap[j].setStatus(secondaryStructureTypes::Bridge);
 252             }
 253             default :
 254                 continue;
 255             }
 256         }
 257     }
 258
 259
 260
 261
 262
 263
 264
 265
 266
 267
 268
 269
 270 //    for (std::size_t i{ 1 }; i < HBondsMap.front().size() - 1; ++i){
 271 //        for (std::size_t j{ 1 }; j < HBondsMap.front().size() - 1; ++j){
 272 //            if (std::abs(static_cast<int>(i) - static_cast<int>(j)) > 2){
 273 //                if ((HBondsMap[i - 1][j] && HBondsMap[j][i + 1])    ||
 274 //                    (HBondsMap[j - 1][i] && HBondsMap[i][j + 1])){
 275 //                    Bridge[i].push_back(j);
 276 //                }
 277 //                if ((HBondsMap[i][j] && HBondsMap[j][i])    ||
 278 //                    (HBondsMap[i - 1][j + 1] && HBondsMap[j - 1][i + 1])){
 279 //                    AntiBridge[i].push_back(j);
 280 //                }
 281 //            }
 282 //        }
 283 //    }
 284 //    for (std::size_t i{ 0 }; i < HBondsMap.front().size(); ++i){
 285 //        if ((!Bridge[i].empty() || !AntiBridge[i].empty())){
 286 //            setStatus(i, secondaryStructureTypes::Bulge);
 287 //        }
 288 //    }
 289 //    for (std::size_t i{ 2 }; i + 2 < HBondsMap.front().size(); ++i){
 290 //        for (std::size_t j { i - 2 }; j <= (i + 2); ++j){
 291 //            if (j == i){
 292 //                continue;
 293 //            }
 294 //            else {
 295 //                for (std::vector<bridgeTypes>::const_iterator bridge {Bridges.begin()}; bridge != Bridges.end(); ++bridge ){
 296 //                    if (!getBridge(*bridge)[i].empty() || !getBridge(*bridge)[j].empty()){
 297 //                        for (std::size_t i_resi{ 0 }; i_resi < getBridge(*bridge)[i].size(); ++i_resi){
 298 //                            for (std::size_t j_resi{ 0 }; j_resi < getBridge(*bridge)[j].size(); ++j_resi){
 299 //                                if (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 300 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 301 //                                        && (abs(static_cast<int>(getBridge(*bridge)[i][i_resi])
 302 //                                        - static_cast<int>(getBridge(*bridge)[j][j_resi]))
 303 //                                        < 5)){
 304 //                                    if (j < i){
 305 //                                        for (std::size_t k{ 0 }; k <= i - j; ++k){
 306 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 307 //                                        }
 308 //                                    }
 309 //                                    else{
 310 //                                        for (std::size_t k{ 0 }; k <= j - i; ++k){
 311 //                                            setStatus(i + k, secondaryStructureTypes::Ladder);
 312 //                                        }
 313 //                                    }
 314 //                                }
 315 //                            }
 316 //                        }
 317 //                    }
 318 //                }
 319 //            }
 320 //        }
 321 //    }
 322 }
 323
 324 void secondaryStructures::analyzeTurnsAndHelicesPatterns(){
 325     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 326         std::size_t stride {static_cast<std::size_t>(i) + 3};
 327         std::cout << "Testing Helix_" << stride << std::endl;
 328         for(std::size_t j {0}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 329             std::cout << "Testing " << j << " and " << j + stride << std::endl;
 330             if ( hasHBondBetween(j + stride, j) && NoChainBreaksBetween(j, j + stride) ){
 331                 std::cout << j << " and " << j + stride << " has hbond!" << std::endl;
 332                 SecondaryStructuresStatusMap[j + stride].setStatus(HelixPositions::End, i);
 333
 334                 for (std::size_t k {1}; k < stride; ++k){
 335                     if( SecondaryStructuresStatusMap[j + k].getStatus(i) == HelixPositions::None ){
 336                         SecondaryStructuresStatusMap[j + k].setStatus(HelixPositions::Middle, i);
 337                         SecondaryStructuresStatusMap[j + k].setStatus(secondaryStructureTypes::Turn);
 338                     }
 339                 }
 340
 341                 if( SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::End ){
 342                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start_AND_End, i);
 343                 }
 344                 else {
 345                     SecondaryStructuresStatusMap[j].setStatus(HelixPositions::Start, i);
 346                 }
 347             }
 348         }
 349     }
 350
 351     for(const turnsTypes &i : { turnsTypes::Turn_4, turnsTypes::Turn_3, turnsTypes::Turn_5 }){
 352         std::size_t stride {static_cast<std::size_t>(i) + 3};
 353         for(std::size_t j {1}; j + stride < SecondaryStructuresStatusMap.size(); ++j){
 354             if ( (SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j - 1].getStatus(i) == HelixPositions::Start_AND_End ) &&
 355                  (SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start || SecondaryStructuresStatusMap[j].getStatus(i) == HelixPositions::Start_AND_End ) ){
 356                 bool empty = true;
 357                 secondaryStructureTypes Helix;
 358                 switch(i){
 359                 case turnsTypes::Turn_3:
 360                     for (std::size_t k {0}; empty && k < stride; ++k){
 361                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_3);
 362                     }
 363                     Helix = secondaryStructureTypes::Helix_3;
 364                     break;
 365                 case turnsTypes::Turn_5:
 366                     for (std::size_t k {0}; empty && k < stride; ++k){
 367                         empty = SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Loop ) || SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_5) || (PiHelixPreference && SecondaryStructuresStatusMap[j + k].getStatus(secondaryStructureTypes::Helix_4)); //TODO
 368                     }
 369                     Helix = secondaryStructureTypes::Helix_5;
 370                     break;
 371                 default:
 372                     Helix = secondaryStructureTypes::Helix_4;
 373                     break;
 374                 }
 375                 if ( empty || Helix == secondaryStructureTypes::Helix_4 ){
 376                     for(std::size_t k {0}; k < stride; ++k ){
 377                         SecondaryStructuresStatusMap[j + k].setStatus(Helix);
 378                     }
 379                 }
 380             }
 381         }
 382     }
 383
 384     /* Не знаю зач они в дссп так сделали, этож полное говно */
 385
 386 //    for(std::size_t i {1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 387 //        if (SecondaryStructuresStatusMap[i].getStatus() == secondaryStructureTypes::Loop || SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Bend)){
 388 //            bool isTurn = false;
 389 //            for(const turnsTypes &j : {turnsTypes::Turn_3, turnsTypes::Turn_4, turnsTypes::Turn_5}){
 390 //                std::size_t stride {static_cast<std::size_t>(j) + 3};
 391 //                for(std::size_t k {1}; k < stride and !isTurn; ++k){
 392 //                    isTurn = (i >= k) && (SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start || SecondaryStructuresStatusMap[i - k].getStatus(j) == HelixPositions::Start_AND_End) ;
 393 //                }
 394 //            }
 395 //            if (isTurn){
 396 //                SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Turn);
 397 //            }
 398 //        }
 399 //    }
 400
 401 }
 402
 403 void secondaryStructures::analyzePPHelicesPatterns(){}
 404
 405 std::string secondaryStructures::patternSearch(){
 406
 407
 408     analyzeBridgesAndLaddersPatterns();
 409     analyzeTurnsAndHelicesPatterns();
 410 //    analyzePPHelicesPatterns();
 411
 412 //    for(std::size_t i {0}; i < ResInfoMap->size(); ++i){
 413 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) << std::endl;
 414 //    }
 415
 416 //    std::cout.precision(5);
 417 //    for(std::size_t i{0}; i < ResInfoMap->size(); ++i, std::cout << std::endl << std::endl){
 418 //        std::cout << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name) ;
 419 //        if ( (*ResInfoMap)[i].donor[0] != nullptr ){
 420 //            std::cout << " has donor[0] = " << (*ResInfoMap)[i].donor[0]->nr << " " << *((*ResInfoMap)[i].donor[0]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[0] << " and" ;
 421 //        }
 422 //        else {
 423 //            std::cout << " has no donor[0] and" ;
 424 //        }
 425 //        if ( (*ResInfoMap)[i].acceptor[0] != nullptr ){
 426 //            std::cout << " has acceptor[0] = " << (*ResInfoMap)[i].acceptor[0]->nr << " " << *((*ResInfoMap)[i].acceptor[0]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[0] ;
 427 //        }
 428 //        else {
 429 //            std::cout << " has no acceptor[0]" ;
 430 //        }
 431 //        std::cout << std::endl << "Also, " << (*ResInfoMap)[i].info->nr << " " << *((*ResInfoMap)[i].info->name);
 432 //        if ( (*ResInfoMap)[i].donor[1] != nullptr ){
 433 //            std::cout << " has donor[1] = " << (*ResInfoMap)[i].donor[1]->nr << " " << *((*ResInfoMap)[i].donor[1]->name) << " with E = " << (*ResInfoMap)[i].donorEnergy[1] << " and" ;
 434 //        }
 435 //        else {
 436 //            std::cout << " has no donor[1] and" ;
 437 //        }
 438 //        if ( (*ResInfoMap)[i].acceptor[1] != nullptr ){
 439 //            std::cout << " has acceptor[1] = " << (*ResInfoMap)[i].acceptor[1]->nr << " " << *((*ResInfoMap)[i].acceptor[1]->name) << " with E = " << (*ResInfoMap)[i].acceptorEnergy[1] ;
 440 //        }
 441 //        else {
 442 //            std::cout << " has no acceptor[1]" ;
 443 //        }
 444 //    }
 445
 446     /*Write Data*/
 447
 448     for(std::size_t i {static_cast<std::size_t>(secondaryStructureTypes::Bend)}; i != static_cast<std::size_t>(secondaryStructureTypes::Count); ++i){
 449         for(std::size_t j {0}; j < SecondaryStructuresStatusMap.size(); ++j){
 450             if (SecondaryStructuresStatusMap[j].getStatus(static_cast<secondaryStructureTypes>(i))){
 451                 SecondaryStructuresStringLine[j] = secondaryStructureTypeNames[i] ;
 452             }
 453         }
 454     }
 455
 456     /*Add breaks*/
 457
 458     if(SecondaryStructuresStatusMap.size() > 1){
 459         for(std::size_t i {0}, linefactor{1}; i + 1 < SecondaryStructuresStatusMap.size(); ++i){
 460             if( SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) && SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break) ){
 461                 if(SecondaryStructuresStatusMap[i].isBreakPartnerWith(&SecondaryStructuresStatusMap[i + 1]) && SecondaryStructuresStatusMap[i + 1].isBreakPartnerWith(&SecondaryStructuresStatusMap[i]) ){
 462                     SecondaryStructuresStringLine.insert(SecondaryStructuresStringLine.begin() + i + linefactor, secondaryStructureTypeNames[secondaryStructureTypes::Break]);
 463                     ++linefactor;
 464                 }
 465             }
 466         }
 467     }
 468     return SecondaryStructuresStringLine;
 469 }
 470
 471 secondaryStructures::~secondaryStructures(){
 472     SecondaryStructuresStatusMap.resize(0);
 473     SecondaryStructuresStringLine.resize(0);
 474 }
 475
 476 DsspTool::DsspStorage::DsspStorage(){
 477     storaged_data.resize(0);
 478 }
 479
 480 void DsspTool::DsspStorage::clearAll(){
 481     storaged_data.resize(0);
 482 }
 483
 484 std::mutex DsspTool::DsspStorage::mx;
 485
 486 void DsspTool::DsspStorage::storageData(int frnr, std::string data){
 487     std::lock_guard<std::mutex> guardian(mx);
 488     std::pair<int, std::string> datapair(frnr, data);
 489     storaged_data.push_back(datapair);
 490 }
 491
 492 std::vector<std::pair<int, std::string>> DsspTool::DsspStorage::returnData(){
 493     std::sort(storaged_data.begin(), storaged_data.end());
 494     return storaged_data;
 495 }
 496
 497 void alternateNeighborhoodSearch::setCutoff(const real &cutoff_init){
 498     cutoff = cutoff_init;
 499 }
 500
 501 void alternateNeighborhoodSearch::FixAtomCoordinates(real &coordinate, const real vector_length){
 502     while (coordinate < 0) {
 503         coordinate += vector_length;
 504     }
 505     while (coordinate >= vector_length) {
 506         coordinate -= vector_length;
 507     }
 508 }
 509
 510 void alternateNeighborhoodSearch::ReCalculatePBC(int &x, const int &x_max) {
 511     if (x < 0) {
 512         x += x_max;
 513     }
 514     if (x >= x_max) {
 515         x -= x_max;
 516     }
 517 }
 518
 519 void alternateNeighborhoodSearch::GetMiniBoxesMap(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 520     rvec coordinates, box_vector_length;
 521     num_of_miniboxes.resize(0);
 522     num_of_miniboxes.resize(3);
 523     for (std::size_t i{XX}; i <= ZZ; ++i) {
 524         box_vector_length[i] = std::sqrt(
 525                     std::pow(fr.box[i][XX], 2) + std::pow(fr.box[i][YY], 2) + std::pow(fr.box[i][ZZ], 2));
 526         num_of_miniboxes[i] = std::floor((box_vector_length[i] / cutoff)) + 1;
 527     }
 528     MiniBoxesMap.resize(0);
 529     MiniBoxesReverseMap.resize(0);
 530     MiniBoxesMap.resize(num_of_miniboxes[XX], std::vector<std::vector<std::vector<std::size_t> > >(
 531                              num_of_miniboxes[YY], std::vector<std::vector<std::size_t> >(
 532                              num_of_miniboxes[ZZ], std::vector<std::size_t>(
 533                              0))));
 534     MiniBoxesReverseMap.resize(IndexMap.size(), std::vector<std::size_t>(3));
 535     for (std::vector<ResInfo>::const_iterator i {IndexMap.begin()}; i != IndexMap.end(); ++i) {
 536         for (std::size_t j{XX}; j <= ZZ; ++j) {
 537             coordinates[j] = fr.x[i->getIndex(backboneAtomTypes::AtomCA)][j];
 538             FixAtomCoordinates(coordinates[j], box_vector_length[j]);
 539         }
 540         MiniBoxesMap[std::floor(coordinates[XX] / cutoff)][std::floor(coordinates[YY] / cutoff)][std::floor(
 541                           coordinates[ZZ] / cutoff)].push_back(i - IndexMap.begin());
 542         for (std::size_t j{XX}; j <= ZZ; ++j){
 543             MiniBoxesReverseMap[i - IndexMap.begin()][j] = std::floor(coordinates[j] / cutoff);
 544         }
 545     }
 546 }
 547
 548 void alternateNeighborhoodSearch::AltPairSearch(const t_trxframe &fr, const std::vector<ResInfo> &IndexMap){
 549     GetMiniBoxesMap(fr, IndexMap);
 550     MiniBoxSize[XX] = MiniBoxesMap.size();
 551     MiniBoxSize[YY] = MiniBoxesMap.front().size();
 552     MiniBoxSize[ZZ] = MiniBoxesMap.front().front().size();
 553     PairMap.resize(0);
 554     PairMap.resize(IndexMap.size(), std::vector<bool>(IndexMap.size(), false));
 555     ResiI = PairMap.begin();
 556     ResiJ = ResiI->begin();
 557
 558     for (std::vector<ResInfo>::const_iterator i = IndexMap.begin(); i != IndexMap.end(); ++i){
 559         for (offset[XX] = -1; offset[XX] <= 1; ++offset[XX]) {
 560             for (offset[YY] = -1; offset[YY] <= 1; ++offset[YY]) {
 561                 for (offset[ZZ] = -1; offset[ZZ] <= 1; ++offset[ZZ]) {
 562                     for (std::size_t k{XX}; k <= ZZ; ++k) {
 563                         fixBox[k] = MiniBoxesReverseMap[i - IndexMap.begin()][k] + offset[k];
 564                         ReCalculatePBC(fixBox[k], MiniBoxSize[k]);
 565                     }
 566                     for (std::size_t j{0}; j < MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]].size(); ++j) {
 567                         if ( (i - IndexMap.begin()) != MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]){
 568                             PairMap[i - IndexMap.begin()][MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]] = true;
 569                             PairMap[MiniBoxesMap[fixBox[XX]][fixBox[YY]][fixBox[ZZ]][j]][i - IndexMap.begin()] = true;
 570                         }
 571                     }
 572                 }
 573             }
 574         }
 575     }
 576 }
 577
 578 bool alternateNeighborhoodSearch::findNextPair(){
 579
 580     if(!PairMap.size()){
 581         return false;
 582     }
 583
 584     for(; ResiI != PairMap.end(); ++ResiI, ResiJ = ResiI->begin() ){
 585         for(; ResiJ != ResiI->end(); ++ResiJ){
 586             if(*ResiJ){
 587                 resiIpos = ResiI - PairMap.begin();
 588                 resiJpos = ResiJ - ResiI->begin();
 589                 if ( ResiJ != ResiI->end() ){
 590                     ++ResiJ;
 591                 }
 592                 else if (ResiI != PairMap.end()) {
 593                     ++ResiI;
 594                     ResiJ = ResiI->begin();
 595                 }
 596                 else {
 597                     return false; // ???
 598                 }
 599                 return true;
 600             }
 601         }
 602     }
 603
 604     return false;
 605 }
 606
 607 std::size_t alternateNeighborhoodSearch::getResiI() const {
 608     return resiIpos;
 609 }
 610
 611 std::size_t alternateNeighborhoodSearch::getResiJ() const {
 612     return resiJpos;
 613 }
 614
 615
 616 DsspTool::DsspStorage DsspTool::Storage;
 617
 618 DsspTool::DsspTool(){
 619 }
 620
 621 void DsspTool::calculateBends(const t_trxframe &fr, const t_pbc *pbc)
 622 {
 623    const float benddegree{ 70.0 }, maxdist{ 2.5 };
 624    float       degree{ 0 }, vdist{ 0 }, vprod{ 0 };
 625    gmx::RVec   a{ 0, 0, 0 }, b{ 0, 0, 0 };
 626    for (std::size_t i{ 0 }; i + 1 < IndexMap.size(); ++i)
 627    {
 628        if (CalculateAtomicDistances(static_cast<int>(IndexMap[i].getIndex(backboneAtomTypes::AtomC)),
 629                                     static_cast<int>(IndexMap[i + 1].getIndex(backboneAtomTypes::AtomN)),
 630                                     fr,
 631                                     pbc)
 632            > maxdist)
 633        {
 634            PatternSearch.SecondaryStructuresStatusMap[i].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i + 1]);
 635            PatternSearch.SecondaryStructuresStatusMap[i + 1].setBreak(&PatternSearch.SecondaryStructuresStatusMap[i]);
 636
 637 //           std::cout << "Break between " << i + 1 << " and " << i + 2 << std::endl;
 638        }
 639    }
 640    for (std::size_t i{ 2 }; i + 2 < IndexMap.size() ; ++i)
 641    {
 642        if (PatternSearch.SecondaryStructuresStatusMap[i - 2].getStatus(secondaryStructureTypes::Break) ||
 643            PatternSearch.SecondaryStructuresStatusMap[i - 1].getStatus(secondaryStructureTypes::Break) ||
 644            PatternSearch.SecondaryStructuresStatusMap[i].getStatus(secondaryStructureTypes::Break) ||
 645            PatternSearch.SecondaryStructuresStatusMap[i + 1].getStatus(secondaryStructureTypes::Break)
 646           )
 647        {
 648            continue;
 649        }
 650        for (int j{ 0 }; j < 3; ++j)
 651        {
 652            a[j] = fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j]
 653                   - fr.x[IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA)][j];
 654            b[j] = fr.x[IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA)][j]
 655                   - fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)][j];
 656        }
 657        vdist = (a[0] * b[0]) + (a[1] * b[1]) + (a[2] * b[2]);
 658        vprod = CalculateAtomicDistances(IndexMap[i - 2].getIndex(backboneAtomTypes::AtomCA),
 659                                         IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 660                                         fr,
 661                                         pbc)
 662                * gmx::c_angstrom / gmx::c_nano
 663                * CalculateAtomicDistances(IndexMap[i].getIndex(backboneAtomTypes::AtomCA),
 664                                           IndexMap[i + 2].getIndex(backboneAtomTypes::AtomCA),
 665                                           fr,
 666                                           pbc)
 667                * gmx::c_angstrom / gmx::c_nano;
 668        degree = std::acos(vdist / vprod) * gmx::c_rad2Deg;
 669        if (degree > benddegree)
 670        {
 671            PatternSearch.SecondaryStructuresStatusMap[i].setStatus(secondaryStructureTypes::Bend);
 672        }
 673    }
 674 }
 675
 676 void DsspTool::calculateHBondEnergy(ResInfo& Donor,
 677                        ResInfo& Acceptor,
 678                        const t_trxframe&          fr,
 679                        const t_pbc*               pbc)
 680 {
 681    /*
 682     * DSSP uses eq from dssp 2.x
 683     * kCouplingConstant = 27.888,  //  = 332 * 0.42 * 0.2
 684     * E = k * (1/rON + 1/rCH - 1/rOH - 1/rCN) where CO comes from one AA and NH from another
 685     * if R is in A
 686     * Hbond if E < -0.5
 687     *
 688     * For the note, H-Bond Donor is N-H («Donor of H») and H-Bond Acceptor is C=O («Acceptor of H»)
 689     *
 690     */
 691
 692     if (CalculateAtomicDistances(
 693                 Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 694         >= minimalCAdistance)
 695     {
 696         return void();
 697     }
 698
 699     const float kCouplingConstant = 27.888;
 700     const float minimalAtomDistance{ 0.5 },
 701             minEnergy{ -9.9 };
 702     float HbondEnergy{ 0 };
 703     float distanceNO{ 0 }, distanceHC{ 0 }, distanceHO{ 0 }, distanceNC{ 0 };
 704
 705 //    std::cout << "For Donor №" << Donor.info->nr - 1 << " and Accpetor №" << Acceptor.info->nr - 1 << std::endl;
 706
 707     if( !(Donor.is_proline) && (Acceptor.getIndex(backboneAtomTypes::AtomC) && Acceptor.getIndex(backboneAtomTypes::AtomO)
 708                                 && Donor.getIndex(backboneAtomTypes::AtomN) && ( Donor.getIndex(backboneAtomTypes::AtomH) || initParams.addHydrogens ) ) ){ // TODO
 709         distanceNO = CalculateAtomicDistances(
 710                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 711         distanceNC = CalculateAtomicDistances(
 712                Donor.getIndex(backboneAtomTypes::AtomN), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 713         if (initParams.addHydrogens){
 714             if (Donor.prevResi != nullptr && Donor.prevResi->getIndex(backboneAtomTypes::AtomC) && Donor.prevResi->getIndex(backboneAtomTypes::AtomO)){
 715                rvec atomH{};
 716                float prevCODist {CalculateAtomicDistances(Donor.prevResi->getIndex(backboneAtomTypes::AtomC), Donor.prevResi->getIndex(backboneAtomTypes::AtomO), fr, pbc)};
 717                for (int i{XX}; i <= ZZ; ++i){
 718                    float prevCO = fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomC)][i] - fr.x[Donor.prevResi->getIndex(backboneAtomTypes::AtomO)][i];
 719                    atomH[i] = fr.x[Donor.getIndex(backboneAtomTypes::AtomH)][i]; // Но на самом деле берутся координаты N
 720                    atomH[i] += prevCO / prevCODist;
 721                }
 722                distanceHO = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 723                distanceHC = CalculateAtomicDistances(atomH, Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 724             }
 725             else{
 726                 distanceHO = distanceNO;
 727                 distanceHC = distanceNC;
 728             }
 729        }
 730        else {
 731            distanceHO = CalculateAtomicDistances(
 732                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomO), fr, pbc);
 733            distanceHC = CalculateAtomicDistances(
 734                    Donor.getIndex(backboneAtomTypes::AtomH), Acceptor.getIndex(backboneAtomTypes::AtomC), fr, pbc);
 735        }
 736        if ((distanceNO < minimalAtomDistance) || (distanceHC < minimalAtomDistance)
 737         || (distanceHO < minimalAtomDistance) || (distanceNC < minimalAtomDistance))
 738        {
 739             HbondEnergy = minEnergy;
 740        }
 741        else{
 742            HbondEnergy =
 743                    kCouplingConstant
 744                    * ((1 / distanceNO) + (1 / distanceHC) - (1 / distanceHO) - (1 / distanceNC));
 745        }
 746
 747 //       std::cout << "CA-CA distance: " << CalculateAtomicDistances(
 748 //                        Donor.getIndex(backboneAtomTypes::AtomCA), Acceptor.getIndex(backboneAtomTypes::AtomCA), fr, pbc) << std::endl;
 749 //       std::cout << "N-O distance: " << distanceNO << std::endl;
 750 //       std::cout << "N-C distance: " << distanceNC << std::endl;
 751 //       std::cout << "H-O distance: " << distanceHO << std::endl;
 752 //       std::cout << "H-C distance: " << distanceHC << std::endl;
 753
 754        HbondEnergy = std::round(HbondEnergy * 1000) / 1000;
 755
 756 //       if ( HbondEnergy < minEnergy ){ // I don't think that this is correct
 757 //            HbondEnergy = minEnergy;
 758 //       }
 759
 760 //       std::cout << "Calculated energy = " << HbondEnergy << std::endl;
 761     }
 762 //    else{
 763 //        std::cout << "Donor Is Proline" << std::endl;
 764 //    }
 765
 766     if (HbondEnergy < Donor.acceptorEnergy[0]){
 767            Donor.acceptor[1] = Donor.acceptor[0];
 768            Donor.acceptor[0] = Acceptor.info;
 769            Donor.acceptorEnergy[0] = HbondEnergy;
 770     }
 771     else if (HbondEnergy < Donor.acceptorEnergy[1]){
 772            Donor.acceptor[1] = Acceptor.info;
 773            Donor.acceptorEnergy[1] = HbondEnergy;
 774     }
 775
 776     if (HbondEnergy < Acceptor.donorEnergy[0]){
 777            Acceptor.donor[1] = Acceptor.donor[0];
 778            Acceptor.donor[0] = Donor.info;
 779            Acceptor.donorEnergy[0] = HbondEnergy;
 780     }
 781     else if (HbondEnergy < Acceptor.donorEnergy[1]){
 782            Acceptor.donor[1] = Donor.info;
 783            Acceptor.donorEnergy[1] = HbondEnergy;
 784     }
 785 }
 786
 787
 788 /* Calculate Distance From B to A */
 789 float DsspTool::CalculateAtomicDistances(const int &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 790 {
 791    gmx::RVec r{ 0, 0, 0 };
 792    pbc_dx(pbc, fr.x[A], fr.x[B], r.as_vec());
 793    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 794 }
 795
 796 /* Calculate Distance From B to A, where A is only fake coordinates */
 797 float DsspTool::CalculateAtomicDistances(const rvec &A, const int &B, const t_trxframe &fr, const t_pbc *pbc)
 798 {
 799    gmx::RVec r{ 0, 0, 0 };
 800    pbc_dx(pbc, A, fr.x[B], r.as_vec());
 801    return r.norm() * gmx::c_nm2A; // НЕ ТРОГАТЬ
 802 }
 803
 804 void DsspTool::initAnalysis(/*const TrajectoryAnalysisSettings &settings,*/const TopologyInformation& top, const initParameters &initParamz)
 805 {
 806    initParams = initParamz;
 807    ResInfo _backboneAtoms;
 808    std::size_t                 i{ 0 };
 809    std::string proLINE;
 810    int resicompare{ top.atoms()->atom[static_cast<std::size_t>(*(initParams.sel_.atomIndices().begin()))].resind };
 811    IndexMap.resize(0);
 812    IndexMap.push_back(_backboneAtoms);
 813    IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 814    proLINE = *(IndexMap[i].info->name);
 815    if( proLINE.compare("PRO") == 0 ){
 816        IndexMap[i].is_proline = true;
 817    }
 818
 819    for (gmx::ArrayRef<const int>::iterator ai{ initParams.sel_.atomIndices().begin() }; (ai != initParams.sel_.atomIndices().end()); ++ai){
 820        if (resicompare != top.atoms()->atom[static_cast<std::size_t>(*ai)].resind)
 821        {
 822            ++i;
 823            resicompare = top.atoms()->atom[static_cast<std::size_t>(*ai)].resind;
 824            IndexMap.emplace_back(_backboneAtoms);
 825            IndexMap[i].info = &(top.atoms()->resinfo[resicompare]);
 826            proLINE = *(IndexMap[i].info->name);
 827            if( proLINE.compare("PRO") == 0 ){
 828                IndexMap[i].is_proline = true;
 829            }
 830
 831        }
 832        std::string atomname(*(top.atoms()->atomname[static_cast<std::size_t>(*ai)]));
 833        if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA])
 834        {
 835            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomCA)] = *ai;
 836        }
 837        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC])
 838        {
 839            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomC)] = *ai;
 840        }
 841        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO])
 842        {
 843            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomO)] = *ai;
 844        }
 845        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN])
 846        {
 847            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomN)] = *ai;
 848            if (initParamz.addHydrogens == true){
 849                IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 850            }
 851        }
 852        else if (atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH] && initParamz.addHydrogens == false) // Юзать водород в структуре
 853        {
 854            IndexMap[i]._backboneIndices[static_cast<std::size_t>(backboneAtomTypes::AtomH)] = *ai;
 855        }
 856
 857
 858
 859 //       if( atomname == backboneAtomTypeNames[backboneAtomTypes::AtomCA] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomC] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomO]
 860 //       || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomN] || atomname == backboneAtomTypeNames[backboneAtomTypes::AtomH]){
 861 //           std::cout << "Atom " << atomname << " №" << *ai << " From Resi " << *(top.atoms()->resinfo[i].name) << " №" << resicompare << std::endl;
 862 //       }
 863    }
 864
 865    for (std::size_t j {1}; j < IndexMap.size(); ++j){
 866        IndexMap[j].prevResi = &(IndexMap[j - 1]);
 867
 868        IndexMap[j - 1].nextResi = &(IndexMap[j]);
 869
 870 //           std::cout << "Resi " << IndexMap[i].info->nr << *(IndexMap[i].info->name) << std::endl;
 871 //           std::cout << "Prev resi is " << IndexMap[i].prevResi->info->nr << *(IndexMap[i].prevResi->info->name) << std::endl;
 872 //           std::cout << "Prev resi's next resi is " << IndexMap[i - 1].nextResi->info->nr << *(IndexMap[i - 1].nextResi->info->name) << std::endl;
 873 //         std::cout << IndexMap[j].prevResi->info->nr;
 874 //         std::cout << *(IndexMap[j].prevResi->info->name) ;
 875 //         std::cout << " have CA = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomCA) ;
 876 //         std::cout << " C = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomC);
 877 //         std::cout << " O = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomO);
 878 //         std::cout << " N = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomN);
 879 //         std::cout << " H = " << IndexMap[j].prevResi->getIndex(backboneAtomTypes::AtomH) << std::endl;
 880    }
 881
 882    nres = i + 1;
 883 }
 884
 885 void DsspTool::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc)
 886 {
 887
 888     switch(initParams.NBS){
 889     case (NBSearchMethod::Classique): {
 890
 891         // store positions of CA atoms to use them for nbSearch
 892         std::vector<gmx::RVec> positionsCA_;
 893         for (std::size_t i{ 0 }; i < IndexMap.size(); ++i)
 894         {
 895             positionsCA_.emplace_back(fr.x[IndexMap[i].getIndex(backboneAtomTypes::AtomCA)]);
 896         }
 897
 898         AnalysisNeighborhood nb_;
 899         nb_.setCutoff(initParams.cutoff_);
 900         AnalysisNeighborhoodPositions       nbPos_(positionsCA_);
 901         gmx::AnalysisNeighborhoodSearch     start      = nb_.initSearch(pbc, nbPos_);
 902         gmx::AnalysisNeighborhoodPairSearch pairSearch = start.startPairSearch(nbPos_);
 903         gmx::AnalysisNeighborhoodPair       pair;
 904         while (pairSearch.findNextPair(&pair))
 905         {
 906             if(CalculateAtomicDistances(
 907                         IndexMap[pair.refIndex()].getIndex(backboneAtomTypes::AtomCA), IndexMap[pair.testIndex()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 908                 < minimalCAdistance){
 909                 calculateHBondEnergy(IndexMap[pair.refIndex()], IndexMap[pair.testIndex()], fr, pbc);
 910                 if (IndexMap[pair.testIndex()].info != IndexMap[pair.refIndex() + 1].info){
 911                     calculateHBondEnergy(IndexMap[pair.testIndex()], IndexMap[pair.refIndex()], fr, pbc);
 912                 }
 913             }
 914         }
 915
 916         break;
 917     }
 918     case (NBSearchMethod::Experimental): { // TODO FIX
 919
 920         alternateNeighborhoodSearch as_;
 921
 922         as_.setCutoff(initParams.cutoff_);
 923
 924         as_.AltPairSearch(fr, IndexMap);
 925
 926         while (as_.findNextPair()){
 927             if(CalculateAtomicDistances(
 928                         IndexMap[as_.getResiI()].getIndex(backboneAtomTypes::AtomCA), IndexMap[as_.getResiJ()].getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 929                 < minimalCAdistance){
 930                 calculateHBondEnergy(IndexMap[as_.getResiI()], IndexMap[as_.getResiJ()], fr, pbc);
 931                 if (IndexMap[as_.getResiJ()].info != IndexMap[as_.getResiI() + 1].info){
 932                     calculateHBondEnergy(IndexMap[as_.getResiJ()], IndexMap[as_.getResiI()], fr, pbc);
 933                 }
 934             }
 935         }
 936
 937         break;
 938     }
 939     default: {
 940
 941         for(std::vector<ResInfo>::iterator Donor {IndexMap.begin()}; Donor != IndexMap.end() ; ++Donor){
 942             for(std::vector<ResInfo>::iterator Acceptor {Donor + 1} ; Acceptor != IndexMap.end() ; ++Acceptor){
 943                 if(CalculateAtomicDistances(
 944                             Donor->getIndex(backboneAtomTypes::AtomCA), Acceptor->getIndex(backboneAtomTypes::AtomCA), fr, pbc)
 945                     < minimalCAdistance){
 946                     calculateHBondEnergy(*Donor, *Acceptor, fr, pbc);
 947                     if (Acceptor != Donor + 1){
 948                         calculateHBondEnergy(*Acceptor, *Donor, fr, pbc);
 949                     }
 950                 }
 951             }
 952         }
 953         break;
 954     }
 955     }
 956
 957
 958 //    for(std::size_t i {0}; i < IndexMap.size(); ++i){
 959 //        std::cout << IndexMap[i].info->nr << " " << *(IndexMap[i].info->name) << std::endl;
 960 //    }
 961
 962    PatternSearch.initiateSearch(IndexMap, initParams.PPHelices);
 963    calculateBends(fr, pbc);
 964    Storage.storageData(frnr, PatternSearch.patternSearch());
 965
 966 }
 967
 968 std::vector<std::pair<int, std::string>> DsspTool::getData(){
 969     return Storage.returnData();
 970 }
 971
 972 } // namespace analysismodules
 973
 974 } // namespace gmx