dope_and_excluded_volume.cpp

/** \example atom/dope_and_excluded_volume.cpp

    This example shows you a way to create a pair score that combines
    IMP::score_functor::Dope and excluded volume (via
    IMP::score_functor::HarmonicLowerBound).
*/

#include <IMP/score_functor/Dope.h>
#include <IMP/score_functor/HarmonicLowerBound.h>
#include <IMP/score_functor/DistancePairScore.h>
#include <IMP/score_functor/SphereDistance.h>
#include <IMP/score_functor/AddScores.h>
#include <IMP/atom/DopePairScore.h>
#include <IMP/atom/Chain.h>
#include <IMP/atom/force_fields.h>
#include <IMP/atom/Atom.h>
#include <IMP/atom/Residue.h>
#include <IMP/base/object_macros.h>
#include <IMP/core/XYZR.h>
#include <IMP/base/flags.h>
#include <IMP/base/nullptr_macros.h>

namespace {
const double dope_threshold = 16;
const double spring_constant = 1;

// create some pairs that can be score with dope
IMP::kernel::ParticleIndexPairs setup_pairs(IMP::kernel::Model *m) {
  IMP::kernel::ParticleIndex rpi = m->add_particle("root");
  IMP::atom::Chain chain = IMP::atom::Chain::setup_particle(m, rpi, 'A');
  IMP::kernel::ParticleIndexes atoms;
  for (unsigned int i = 0; i < 2; ++i) {
    IMP::kernel::ParticleIndex rpi = m->add_particle("residue");
    IMP::atom::Residue residue =
        IMP::atom::Residue::setup_particle(m, rpi, IMP::atom::ALA, i);
    chain.add_child(residue);

    IMP::kernel::ParticleIndex api = m->add_particle("atom");
    IMP::atom::Atom atom =
        IMP::atom::Atom::setup_particle(m, api, IMP::atom::AT_CA);
    IMP::algebra::Vector3D coords(0, 10 * i, 0);
    IMP::core::XYZ::setup_particle(m, api, coords);
    residue.add_child(atom);
    atoms.push_back(api);
  }

  // add Dope atom types
  IMP::atom::add_radii(chain);
  IMP::atom::add_dope_score_data(chain);

  IMP::kernel::ParticleIndexPairs all_pairs;
  for (unsigned int i = 0; i < atoms.size(); ++i) {
    for (unsigned int j = 0; j < i; ++j) {
      all_pairs.push_back(IMP::kernel::ParticleIndexPair(atoms[i], atoms[j]));
    }
  }
  return all_pairs;
}
}

int main(int argc, char *argv[]) {
  try {
    // do normal IMP initialization of command line arguments
    // Run with --help to see options.
    IMP::base::setup_from_argv(argc, argv,
                               "Show to to use dope and excluded volume");

    typedef IMP::score_functor::HarmonicLowerBound Harmonic;
    typedef IMP::score_functor::SphereDistance<Harmonic> SoftSphere;
    typedef IMP::score_functor::AddScores<IMP::score_functor::Dope, SoftSphere>
        Score;
    typedef IMP::score_functor::DistancePairScore<Score>
        DopeAndExcludedVolumeDistancePairScore;

    // create one
    IMP::base::PointerMember<DopeAndExcludedVolumeDistancePairScore> score =
        new DopeAndExcludedVolumeDistancePairScore(
            Score(IMP::score_functor::Dope(dope_threshold),
                  SoftSphere(Harmonic(spring_constant))));

    // Now let's use it
    IMP::base::PointerMember<IMP::kernel::Model> model = new IMP::kernel::Model();
    IMP::kernel::ParticleIndexPairs pips = setup_pairs(model);

    for (unsigned int i = 0; i < pips.size(); ++i) {
      std::cout << "Score is " << score->evaluate_index(
                                      model, pips[i], IMP_NULLPTR) << std::endl;
    }
    return 0;
  }
  catch (const std::exception & e) {
    std::cerr << "ERROR: " << e.what() << std::endl;
    return 1;
  }
}