Esempio n. 1
0
float get_actual_radius_of_gyration(kernel::ParticlesTemp ps) {
  algebra::Vector3D cm(0,0,0);
  for (unsigned int i=0; i< ps.size(); ++i) {
    cm+= core::XYZ(ps[i]).get_coordinates();
  }
  cm/=ps.size();
  double ret=0;
  for (unsigned int i=0; i < ps.size(); ++i) {
    double d= get_distance(core::XYZ(ps[i]).get_coordinates(),cm);
    ret+= d;
  }
  return ret/ps.size();
}
Esempio n. 2
0
void ConnectivityRestraint::add_particles(const kernel::ParticlesTemp &ps) {
  if (!sc_ && !ps.empty()) {
    sc_ = new IMP::internal::InternalListSingletonContainer(
        ps[0]->get_model(), "connectivity list");
  }
  get_list(sc_)->add(IMP::internal::get_index(ps));
}
Esempio n. 3
0
IMPCORE_BEGIN_NAMESPACE

FixedRefiner::FixedRefiner(const kernel::ParticlesTemp &ps)
    : Refiner("FixedRefiner%d"), ps_(ps) {
  IMP_LOG_VERBOSE("Created fixed particle refiner with "
                  << ps.size() << " particles" << std::endl);
}
Esempio n. 4
0
void CollisionCrossSection::set_model_particles(
    const kernel::ParticlesTemp &ps) {

  IMP_LOG_TERSE("CollisionCrossSection: kernel::Model particles set"
                << std::endl);

  for (unsigned int i = 0; i < ps.size(); ++i) {
    IMP_USAGE_CHECK(
        (core::XYZR::get_is_setup(ps[i]) && atom::Mass::get_is_setup(ps[i])),
        "Particle " << i << " does not have the required attributes"
                    << std::endl);
  }
  masks_manager_->create_masks(ps);
  // Compute projections
  collision_cross_section_ = 0.0;
  for (unsigned int i = 0; i < n_projections_; ++i) {
    ProjectingOptions options(pixel_size_, resolution_);
    do_project_particles(ps, average_projection_, regs_[i].get_rotation(),
                         pixel_size_ * regs_[i].get_shift_3d(), options,
                         masks_manager_);
    collision_cross_section_ += get_projected_area(average_projection_);
  }
  collision_cross_section_ /= static_cast<double>(n_projections_);
  particles_set_ = true;
}
Esempio n. 5
0
Selection::Selection(const kernel::ParticlesTemp &h) : radius_(-1) {
  if (h.empty()) {
    m_ = nullptr;
    return;
  } else {
    set_hierarchies(h[0]->get_model(), IMP::get_indexes(h));
  }
}
Esempio n. 6
0
ExampleSubsetFilterTable::ExampleSubsetFilterTable(
    unsigned int max_diff, const kernel::ParticlesTemp& ps)
    : domino::SubsetFilterTable("ExampleSubsetFilterTable%1%"),
      max_diff_(max_diff),
      ps_(ps.begin(), ps.end()) {}
Esempio n. 7
0
/** Take a set of core::XYZR particles and relax them relative to a set of
    restraints. Excluded volume is handle separately, so don't include it
in the passed list of restraints. */
void optimize_balls(const kernel::ParticlesTemp &ps, const kernel::RestraintsTemp &rs,
                    const PairPredicates &excluded,
                    const OptimizerStates &opt_states, base::LogLevel ll) {
    // make sure that errors and log messages are marked as coming from this
    // function
    IMP_FUNCTION_LOG;
    base::SetLogState sls(ll);
    IMP_ALWAYS_CHECK(!ps.empty(), "No kernel::Particles passed.", ValueException);
    kernel::Model *m = ps[0]->get_model();
    //double scale = core::XYZR(ps[0]).get_radius();

    IMP_NEW(core::SoftSpherePairScore, ssps, (10));
    IMP_NEW(core::ConjugateGradients, cg, (m));
    cg->set_optimizer_states(opt_states);
    {
        // set up restraints for cg
        IMP_NEW(container::ListSingletonContainer, lsc, (ps));
        IMP_NEW(container::ClosePairContainer, cpc,
                (lsc, 0, core::XYZR(ps[0]).get_radius()));
        cpc->add_pair_filters(excluded);
        base::Pointer<kernel::Restraint> r
            = container::create_restraint(ssps.get(), cpc.get());
        cg->set_scoring_function(rs + kernel::RestraintsTemp(1, r.get()));
        cg->set_optimizer_states(opt_states);
    }
    IMP_NEW(core::MonteCarlo, mc, (m));
    mc->set_optimizer_states(opt_states);
    IMP_NEW(core::IncrementalScoringFunction, isf, (ps, rs));
    {
        // set up MC
        mc->add_mover(create_serial_mover(ps));
        // we are special casing the nbl term for montecarlo, but using all for CG
        mc->set_incremental_scoring_function(isf);
        // use special incremental support for the non-bonded part
        isf->add_close_pair_score(ssps, 0, ps, excluded);
        // make pointer vector
    }

    IMP_LOG_PROGRESS("Performing initial optimization" << std::endl);
    {
        boost::ptr_vector<ScopedSetFloatAttribute> attrs;
        for (unsigned int j = 0; j < attrs.size(); ++j) {
            attrs.push_back(
                new ScopedSetFloatAttribute(ps[j], core::XYZR::get_radius_key(), 0));
        }
        cg->optimize(1000);
    }
    // shrink each of the particles, relax the configuration, repeat
    for (int i = 0; i < 11; ++i) {
        boost::ptr_vector<ScopedSetFloatAttribute> attrs;
        double factor = .1 * i;
        IMP_LOG_PROGRESS("Optimizing with radii at " << factor << " of full"
                         << std::endl);
        for (unsigned int j = 0; j < ps.size(); ++j) {
            attrs.push_back(
                new ScopedSetFloatAttribute(ps[j], core::XYZR::get_radius_key(),
                                            core::XYZR(ps[j]).get_radius() * factor));
        }
        // changed all radii
        isf->set_moved_particles(isf->get_movable_indexes());
        for (int j = 0; j < 5; ++j) {
            mc->set_kt(100.0 / (3 * j + 1));
            mc->optimize(ps.size() * (j + 1) * 100);
            double e = cg->optimize(10);
            IMP_LOG_PROGRESS("Energy is " << e << std::endl);
            if (e < .000001) break;
        }
    }
}