api/nblib/molecules.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements nblib Molecule
  38  *
  39  * \author Victor Holanda <victor.holanda@cscs.ch>
  40  * \author Joe Jordan <ejjordan@kth.se>
  41  * \author Prashanth Kanduri <kanduri@cscs.ch>
  42  * \author Sebastian Keller <keller@cscs.ch>
  43  * \author Artem Zhmurov <zhmurov@gmail.com>
  44  */
  45 #include <algorithm>
  46 #include <tuple>
  47
  48 #include "nblib/exception.h"
  49 #include "nblib/molecules.h"
  50 #include "nblib/particletype.h"
  51 #include "nblib/util/internal.h"
  52
  53 namespace nblib
  54 {
  55
  56
  57 Molecule::Molecule(MoleculeName moleculeName) : name_(std::move(moleculeName)) {}
  58
  59 MoleculeName Molecule::name() const
  60 {
  61     return name_;
  62 }
  63
  64 Molecule& Molecule::addParticle(const ParticleName& particleName,
  65                                 const ResidueName&  residueName,
  66                                 const Charge&       charge,
  67                                 ParticleType const& particleType)
  68 {
  69     auto found = particleTypes_.find(particleType.name());
  70     if (found == particleTypes_.end())
  71     {
  72         particleTypes_.insert(std::make_pair(particleType.name(), particleType));
  73     }
  74     else
  75     {
  76         if (!(found->second == particleType))
  77         {
  78             throw InputException(
  79                     "Differing ParticleTypes with identical names encountered in the same "
  80                     "molecule.");
  81         }
  82     }
  83
  84     particles_.emplace_back(ParticleData{ particleName, residueName, particleType.name(), charge });
  85
  86     // Add self exclusion. We just added the particle, so we know its index and that the exclusion doesn't exist yet
  87     std::size_t id = particles_.size() - 1;
  88     exclusions_.emplace_back(id, id);
  89
  90     return *this;
  91 }
  92
  93 Molecule& Molecule::addParticle(const ParticleName& particleName,
  94                                 const ResidueName&  residueName,
  95                                 ParticleType const& particleType)
  96 {
  97     addParticle(particleName, residueName, Charge(0), particleType);
  98
  99     return *this;
 100 }
 101
 102 Molecule& Molecule::addParticle(const ParticleName& particleName,
 103                                 const Charge&       charge,
 104                                 ParticleType const& particleType)
 105 {
 106     addParticle(particleName, ResidueName(name_), charge, particleType);
 107
 108     return *this;
 109 }
 110
 111 Molecule& Molecule::addParticle(const ParticleName& particleName, const ParticleType& particleType)
 112 {
 113     addParticle(particleName, ResidueName(name_), Charge(0), particleType);
 114
 115     return *this;
 116 }
 117
 118 int Molecule::numParticlesInMolecule() const
 119 {
 120     return particles_.size();
 121 }
 122
 123 void Molecule::addExclusion(const int particleIndex, const int particleIndexToExclude)
 124 {
 125     // We do not need to add exclusion in case the particle indexes are the same
 126     // because self exclusion are added by addParticle
 127     if (particleIndex != particleIndexToExclude)
 128     {
 129         exclusions_.emplace_back(particleIndex, particleIndexToExclude);
 130         exclusions_.emplace_back(particleIndexToExclude, particleIndex);
 131     }
 132 }
 133
 134 void Molecule::addExclusion(std::tuple<std::string, std::string> particle,
 135                             std::tuple<std::string, std::string> particleToExclude)
 136 {
 137     // duplication for the swapped pair happens in getExclusions()
 138     exclusionsByName_.emplace_back(std::make_tuple(std::get<0>(particle), std::get<1>(particle),
 139                                                    std::get<0>(particleToExclude),
 140                                                    std::get<1>(particleToExclude)));
 141 }
 142
 143 void Molecule::addExclusion(const std::string& particleName, const std::string& particleNameToExclude)
 144 {
 145     addExclusion(std::make_tuple(particleName, name_), std::make_tuple(particleNameToExclude, name_));
 146 }
 147
 148 const ParticleType& Molecule::at(const std::string& particleTypeName) const
 149 {
 150     return particleTypes_.at(particleTypeName);
 151 }
 152
 153 ParticleName Molecule::particleName(int i) const
 154 {
 155     return ParticleName(particles_[i].particleName_);
 156 }
 157
 158 ResidueName Molecule::residueName(int i) const
 159 {
 160     return ResidueName(particles_[i].residueName_);
 161 }
 162
 163 std::vector<std::tuple<int, int>> Molecule::getExclusions() const
 164 {
 165     // tuples of (particleName, residueName, index)
 166     std::vector<std::tuple<std::string, std::string, int>> indexKey;
 167     indexKey.reserve(numParticlesInMolecule());
 168
 169     for (int i = 0; i < numParticlesInMolecule(); ++i)
 170     {
 171         indexKey.emplace_back(particles_[i].particleName_, particles_[i].residueName_, i);
 172     }
 173
 174     std::sort(std::begin(indexKey), std::end(indexKey));
 175
 176     std::vector<std::tuple<int, int>> ret = exclusions_;
 177     ret.reserve(exclusions_.size() + exclusionsByName_.size());
 178
 179     // normal operator<, except ignore third element
 180     auto sortKey = [](const auto& tup1, const auto& tup2) {
 181         if (std::get<0>(tup1) < std::get<0>(tup2))
 182         {
 183             return true;
 184         }
 185         else
 186         {
 187             return std::get<1>(tup1) < std::get<1>(tup2);
 188         }
 189     };
 190
 191     // convert exclusions given by names to indices and append
 192     for (auto& tup : exclusionsByName_)
 193     {
 194         const std::string& particleName1 = std::get<0>(tup);
 195         const std::string& residueName1  = std::get<1>(tup);
 196         const std::string& particleName2 = std::get<2>(tup);
 197         const std::string& residueName2  = std::get<3>(tup);
 198
 199         // look up first index (binary search)
 200         auto it1 = std::lower_bound(std::begin(indexKey), std::end(indexKey),
 201                                     std::make_tuple(particleName1, residueName2, 0), sortKey);
 202
 203         // make sure we have the (particleName,residueName) combo
 204         if (it1 == std::end(indexKey) or std::get<0>(*it1) != particleName1 or std::get<1>(*it1) != residueName1)
 205         {
 206             throw std::runtime_error(
 207                     (std::string("Particle ") += particleName1 + std::string(" in residue ") +=
 208                      residueName1 + std::string(" not found in list of particles\n")));
 209         }
 210
 211         int firstIndex = std::get<2>(*it1);
 212
 213         // look up second index (binary search)
 214         auto it2 = std::lower_bound(std::begin(indexKey), std::end(indexKey),
 215                                     std::make_tuple(particleName2, residueName2, 0), sortKey);
 216
 217         // make sure we have the (particleName,residueName) combo
 218         if (it2 == std::end(indexKey) or std::get<0>(*it2) != particleName2 or std::get<1>(*it2) != residueName2)
 219         {
 220             throw std::runtime_error(
 221                     (std::string("Particle ") += particleName2 + std::string(" in residue ") +=
 222                      residueName2 + std::string(" not found in list of particles\n")));
 223         }
 224
 225         int secondIndex = std::get<2>(*it2);
 226
 227         ret.emplace_back(firstIndex, secondIndex);
 228         ret.emplace_back(secondIndex, firstIndex);
 229     }
 230
 231     std::sort(std::begin(ret), std::end(ret));
 232
 233     auto uniqueEnd = std::unique(std::begin(ret), std::end(ret));
 234     if (uniqueEnd != std::end(ret))
 235     {
 236         printf("[nblib] Warning: exclusionList for molecule %s contained duplicates",
 237                name_.value().c_str());
 238     }
 239
 240     ret.erase(uniqueEnd, std::end(ret));
 241     return ret;
 242 }
 243
 244 std::unordered_map<std::string, ParticleType> Molecule::particleTypesMap() const
 245 {
 246     return particleTypes_;
 247 }
 248
 249 std::vector<ParticleData> Molecule::particleData() const
 250 {
 251     return particles_;
 252 }
 253
 254 } // namespace nblib