creating_restraints.h

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/**
 *  \file IMP/example/creating_restraints.h
 *  \brief A simple unary function.
 *
 *  Copyright 2007-2020 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPEXAMPLE_CREATING_RESTRAINTS_H
#define IMPEXAMPLE_CREATING_RESTRAINTS_H

#include <IMP/example/example_config.h>
#include <IMP/container/ClosePairContainer.h>
#include <IMP/container/generic.h>
#include <IMP/container/ConsecutivePairContainer.h>
#include <IMP/container/ListSingletonContainer.h>
#include <IMP/core/SphereDistancePairScore.h>
#include <IMP/core/DistancePairScore.h>

IMPEXAMPLE_BEGIN_NAMESPACE

/** Restrain the passed particles to be connected in a chain. The distance
    between consecutive particles is length_factor*the sum of the radii.

    Note, this assumes that all such chains will be disjoint and so you can
    use the container::ExclusiveConsecutivePairFilter if you want to filter
    out all pairs of particles connected by such chain restraints.

    The restraint is not added to the model.
*/
inline Restraint *create_chain_restraint(Model *m,
    const ParticleIndexes &ps, double length_factor, double k,
    std::string name) {
  IMP_USAGE_CHECK(!ps.empty(), "No ParticleIndexes passed.");
  double scale = core::XYZR(m, ps[0]).get_radius();
  IMP_NEW(core::HarmonicDistancePairScore, hdps,
          (length_factor * 2.0 * scale, k, "chain linker %1%"));
  // Exclusive means that the particles will be in no other
  // ConsecutivePairContainer
  // this assumption accelerates certain computations
  IMP_NEW(container::ExclusiveConsecutivePairContainer, cpc,
          (m, ps, name + " consecutive pairs"));
  Pointer<Restraint> r =
      container::create_restraint(hdps.get(), cpc.get(), "chain restraint %1%");
  // make sure it is not freed
  return r.release();
}

/** Create an excluded-volume style ClosePairsContainer based score. */
inline Restraint *create_excluded_volume(
    Model *m, const ParticleIndexes &ps, double k, std::string name) {
  IMP_USAGE_CHECK(!ps.empty(), "No ParticleIndexes passed.");
  //Model *m = ps[0]->get_model();
  double scale = core::XYZR(m, ps[0]).get_radius();
  IMP_NEW(container::ListSingletonContainer, cores_container,
          (m, ps, name + " list"));
  // Create a close pair container, with a distance bound of 0 and a slack
  // that is proportional to the particle radius
  IMP_NEW(container::ClosePairContainer, cpc, (cores_container, 0, scale * .3));
  IMP_NEW(core::SoftSpherePairScore, hlb, (k));
  Pointer<Restraint> r =
      container::create_restraint(hlb.get(), cpc.get());
  return r.release();
}

IMPEXAMPLE_END_NAMESPACE

#endif /* IMPEXAMPLE_CREATING_RESTRAINTS_H */