Esempi in C++ (Cpp) per ParticleIndexPairs

Esempio n. 1

File: PairContainerSet.cpp Progetto: andreyto/imp-fork-proddl

ParticleIndexPairs PairContainerSet::get_all_possible_indexes() const {
  ParticleIndexPairs sum;
  for (PairContainerConstIterator it= pair_containers_begin();
       it != pair_containers_end(); ++it) {
    ParticleIndexPairs cur=(*it)->get_all_possible_indexes();
    sum.insert(sum.end(), cur.begin(), cur.end());
  }
  return sum;
}

Esempio n. 2

File: ConnectivityRestraint.cpp Progetto: j-ma-bu-l-l-ock/imp

double ConnectivityRestraint::unprotected_evaluate(DerivativeAccumulator *accum)
    const {
  IMP_CHECK_OBJECT(ps_.get());
  IMP_OBJECT_LOG;
  Vector<Edge> mst;
  if (!sc_) return 0;
  ParticleIndexPairs edges = get_edges(sc_, ps_);
  return ps_->evaluate_indexes(get_model(), edges, accum, 0, edges.size());
}

Esempio n. 3

File: AllPairContainer.cpp Progetto: j-ma-bu-l-l-ock/imp

ParticleIndexPairs AllPairContainer::get_range_indexes() const {
  ParticleIndexes ia = c_->get_range_indexes();
  ParticleIndexPairs ret;
  ret.reserve(ia.size() * (ia.size() - 1) / 2);
  for (unsigned int i = 0; i < ia.size(); ++i) {
    for (unsigned int j = 0; j < i; ++j) {
      ret.push_back(ParticleIndexPair(ia[i], ia[j]));
    }
  }
  return ret;
}

Esempio n. 4

File: incremental_scoring_function.cpp Progetto: salilab/imp

ParticleIndexPairs DummyPairContainer::get_range_indexes() const {
  ParticleIndexes pis = c_->get_range_indexes();
  ParticleIndexPairs ret;
  ret.reserve(pis.size() * (pis.size() - 1) / 2);
  for (unsigned int i = 0; i < pis.size(); ++i) {
    for (unsigned int j = 0; j < i; ++j) {
      ret.push_back(ParticleIndexPair(pis[i], pis[j]));
    }
  }
  return ret;
}

Esempio n. 5

File: CoreCloseBipartitePairContainer.cpp Progetto: andreyto/imp-fork-proddl

ParticleIndexPairs
CoreCloseBipartitePairContainer::get_all_possible_indexes() const {
  ParticleIndexes pis= sc_[0]->get_all_possible_indexes();
  ParticleIndexes pjs= sc_[1]->get_all_possible_indexes();
  ParticleIndexPairs ret; ret.reserve(pis.size()*pjs.size());
  for (unsigned int i=0; i< pis.size(); ++i) {
    for (unsigned int j=0; j< pjs.size(); ++j) {
      ret.push_back(ParticleIndexPair(pis[i], pjs[j]));
    }
  }
  return ret;
}

Esempio n. 6

File: BondPairContainer.cpp Progetto: AljGaber/imp

ParticleIndexPairs BondPairContainer::get_range_indexes() const {
  ParticleIndexes ia = sc_->get_range_indexes();
  ParticleIndexPairs ret;
  ret.reserve(ia.size());
  for (unsigned int i = 0; i < ia.size(); ++i) {
    Bond b(get_model(), ia[i]);
    ret.push_back(
        ParticleIndexPair(b.get_bonded(0).get_particle_index(),
                                  b.get_bonded(1).get_particle_index()));
  }
  return ret;
}

Esempio n. 7

File: QuadraticClosePairsFinder.cpp Progetto: j-ma-bu-l-l-ock/imp

ParticleIndexPairs QuadraticClosePairsFinder::get_close_pairs(
    Model *m, const ParticleIndexes &pt) const {
  set_was_used(true);
  IMP_OBJECT_LOG;
  IMP_LOG_TERSE("Adding close pairs from "
                << pt.size() << " particles with threshold " << get_distance()
                << std::endl);
  ParticleIndexPairs ret;
  for (unsigned int i = 0; i < pt.size(); ++i) {
    for (unsigned int j = 0; j < i; ++j) {
      if (get_are_close(m, pt[i], pt[j])) {
        ret.push_back(ParticleIndexPair(pt[i], pt[j]));
      }
    }
  }
  return ret;
}

Esempio n. 8

File: QuadraticClosePairsFinder.cpp Progetto: j-ma-bu-l-l-ock/imp

ParticleIndexPairs QuadraticClosePairsFinder::get_close_pairs(
    Model *m, const ParticleIndexes &pta,
    const ParticleIndexes &ptb) const {
  set_was_used(true);
  IMP_OBJECT_LOG;
  IMP_LOG_TERSE("Quadratic add_close_pairs called with "
                << pta.size() << " and " << ptb.size() << std::endl);
  ParticleIndexPairs ret;
  for (unsigned int i = 0; i < pta.size(); ++i) {
    for (unsigned int j = 0; j < ptb.size(); ++j) {
      if (get_are_close(m, pta[i], ptb[j])) {
        ret.push_back(ParticleIndexPair(pta[i], ptb[j]));
      }
    }
  }
  return ret;
}