ConnectivityRestraint.h

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/**
 *  \file IMP/core/ConnectivityRestraint.h    \brief Connectivity restraint.
 *
 *  Restrict max distance between at least one pair of particles of any
 *  two distinct types.
 *
 *  Copyright 2007-2017 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPCORE_CONNECTIVITY_RESTRAINT_H
#define IMPCORE_CONNECTIVITY_RESTRAINT_H

#include <IMP/core/core_config.h>
#include "DistanceRestraint.h"

#include <IMP/SingletonContainer.h>
#include <IMP/Restraint.h>
#include <IMP/PairScore.h>

IMPCORE_BEGIN_NAMESPACE

//! Ensure that a set of particles remains connected with one another.
/** The restraint implements ambiguous connectivity. That is, it takes
    several particles and ensures that they remain
    connected, but allows how they are connected to change. If you wish
    to restrain the connectivity of sets of
    particles (e.g. each protein is represented using a set of balls)
    use an appropriate PairScore which calls a Refiner (such
    as ClosePairsPairScore).

    \include connectivity_restraint.py

    More precisely, the restraint scores by computing the minimum spanning
    tree  on the complete graph connecting all the particles. The edge
    weights are given by the value of the PairScore for the two endpoints
    of the edge.
 */
class IMPCOREEXPORT ConnectivityRestraint : public Restraint {
  IMP::PointerMember<PairScore> ps_;
  IMP::PointerMember<SingletonContainer> sc_;

 public:
  //! Use the given PairScore
  ConnectivityRestraint(PairScore *ps, SingletonContainerAdaptor sc);

  //! Return the set of pairs which are connected by the restraint
  /** This set of pairs reflects the current configuration at the time of
      the get_connected_pairs() call, not the set at the time of the last
      evaluate() call.
  */
  ParticleIndexPairs get_connected_index_pairs() const;

#ifndef IMP_DOXYGEN
  IMPCORE_DEPRECATED_METHOD_DECL(2.7)
  ParticlePairsTemp get_connected_pairs() const {
    IMPCORE_DEPRECATED_METHOD_DEF(2.7,
                                  "Use get_connected_index_pairs() instead");
    return IMP::internal::get_particle(get_model(),
                                       get_connected_index_pairs());
  }
#endif

  //! Return the pair score used for scoring
  PairScore *get_pair_score() const { return ps_; }

  Restraints do_create_current_decomposition() const;

 public:
  double unprotected_evaluate(IMP::DerivativeAccumulator *accum) const
      IMP_OVERRIDE;
  IMP::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
  IMP_OBJECT_METHODS(ConnectivityRestraint);
  ;
};

IMPCORE_END_NAMESPACE

#endif /* IMPCORE_CONNECTIVITY_RESTRAINT_H */