SphereDistancePairScore.h

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/**
 *  \file IMP/core/SphereDistancePairScore.h
 *  \brief A score on the distance between the surfaces of two spheres.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 */

#ifndef IMPCORE_SPHERE_DISTANCE_PAIR_SCORE_H
#define IMPCORE_SPHERE_DISTANCE_PAIR_SCORE_H

#include <IMP/core/core_config.h>
#include "XYZR.h"
#include <IMP/score_functor/UnaryFunctionEvaluate.h>
#include <IMP/score_functor/SphereDistance.h>
#include <IMP/score_functor/Shift.h>
#include <IMP/score_functor/Harmonic.h>
#include <IMP/score_functor/HarmonicLowerBound.h>
#include <IMP/score_functor/HarmonicUpperBound.h>
#include <IMP/score_functor/distance_pair_score_macros.h>

IMPCORE_BEGIN_NAMESPACE

// needed to keep swig from getting confused or breaking line
// lengths
typedef score_functor::SphereDistance<score_functor::UnaryFunctionEvaluate>
    SphereDistanceScore;

//! A score on the distance between the surfaces of two spheres.
/** Scores based on the distance between the surfaces of two spheres,
    implicitly assuming they are decorated as XYZR, using an arbitrary
    unary function. Note the distance may be negative if the spheres overlap.

    \see XYZR
    \see SphereDistancePairScore
    \see DistancePairScore
    \see SoftSpherePairScore
 */
IMP_FUNCTOR_DISTANCE_PAIR_SCORE(SphereDistancePairScore, SphereDistanceScore,
                                (UnaryFunction *uf,
                                 std::string name =
                                     "SphereDistancePairScore%1%"),
                                (score_functor::UnaryFunctionEvaluate(uf)), );

typedef score_functor::SphereDistance<score_functor::Shift<
    score_functor::HarmonicUpperBound> > HarmonicUpperBoundSphereDistanceScore;

//!A harmonic upper bound on the distance between two spheres
/** \see XYZR
    \see SpherePairScore
    \see SoftSpherePairScore
 */
IMP_FUNCTOR_DISTANCE_PAIR_SCORE(
    HarmonicUpperBoundSphereDistancePairScore,
    HarmonicUpperBoundSphereDistanceScore,
    (double x0, double k,
     std::string name = "HarmonicUpperBoundSphereDistancePairScore%1%"),
    (score_functor::Shift<score_functor::HarmonicUpperBound>(
        x0, score_functor::HarmonicUpperBound(k))), );

//!A harmonic upper bound on the diameter of the span of two spheres
/** This restraint restraints how far the furthest points of two spheres
    are from one another.

    \see XYZR
    \see SpherePairScore
    \see SoftSpherePairScore
    \see NormalizedSphereDistancePairScore
 */
class IMPCOREEXPORT HarmonicUpperBoundSphereDiameterPairScore
    : public PairScore {
  double x0_, k_;

 public:
  HarmonicUpperBoundSphereDiameterPairScore(double d0, double k);
  double get_rest_length() const { return x0_; }
  double get_stiffness() const { return k_; }
  double evaluate_index(Model *m, const ParticleIndexPair &p,
                        DerivativeAccumulator *da) const override;
  ModelObjectsTemp do_get_inputs(
      Model *m, const ParticleIndexes &pis) const override;
  IMP_PAIR_SCORE_METHODS(HarmonicUpperBoundSphereDiameterPairScore);
  IMP_OBJECT_METHODS(HarmonicUpperBoundSphereDiameterPairScore);
};

IMP_OBJECTS(HarmonicUpperBoundSphereDiameterPairScore,
            HarmonicUpperBoundSphereDiameterPairScores);

typedef score_functor::SphereDistance<
    score_functor::Shift<score_functor::Harmonic> > HarmonicSphereDistanceScore;

//! A harmonic score on the distance between two spheres
/** A harmonic score on the distance between two spheres, implicitly
    assuming they are decorated as XYZR.

    \see XYZR
    \see SpherePairScore
    \see SoftSpherePairScore
 */
IMP_FUNCTOR_DISTANCE_PAIR_SCORE(HarmonicSphereDistancePairScore,
    HarmonicSphereDistanceScore,
    (double x0, double k,
     std::string name = "HarmonicSphereDistancePairScore%1%"),
    (score_functor::Shift<score_functor::Harmonic>(
                            x0, score_functor::Harmonic(k))),
    double get_x0() const { return get_score_functor().get_x0(); }
    double get_k() const { return get_score_functor().get_k(); });
IMP_OBJECTS(HarmonicSphereDistancePairScore, HarmonicSphereDistancePairScores);

#ifndef IMP_DOXYGEN
inline double HarmonicUpperBoundSphereDiameterPairScore::evaluate_index(
    Model *m, const ParticleIndexPair &p,
    DerivativeAccumulator *da) const {
  algebra::Vector3D delta =
      m->get_sphere(std::get<0>(p)).get_center()
      - m->get_sphere(std::get<1>(p)).get_center();
  static const double MIN_DISTANCE = .00001;
  double distance = delta.get_magnitude();
  double shifted_distance
        = distance - x0_ + m->get_sphere(std::get<0>(p)).get_radius() +
                           m->get_sphere(std::get<1>(p)).get_radius();
  if (shifted_distance < 0) return 0;
  double score = .5 * k_ * square(shifted_distance);
  if (da && distance > MIN_DISTANCE) {
    double deriv = k_ * shifted_distance;
    algebra::Vector3D uv = delta / distance;
    m->add_to_coordinate_derivatives(std::get<0>(p), uv * deriv, *da);
    m->add_to_coordinate_derivatives(std::get<1>(p), -uv * deriv, *da);
  }
  return score;
}
#endif

//! A score on the normalized distance between the surfaces of two spheres
/** The distance between the surfaces of the two spheres is divided by the
    smaller radius to normalize it.
    \see SphereDistancePairScore
    \see XYZR
    \see DistancePairScore
 */
class IMPCOREEXPORT NormalizedSphereDistancePairScore : public PairScore {
  IMP::PointerMember<UnaryFunction> f_;
  FloatKey radius_;

 public:
  NormalizedSphereDistancePairScore(UnaryFunction *f,
                                    FloatKey radius = FloatKey("radius"));
  virtual double evaluate_index(Model *m,
                                const ParticleIndexPair &p,
                                DerivativeAccumulator *da) const override;
  virtual ModelObjectsTemp do_get_inputs(
      Model *m, const ParticleIndexes &pis) const override;
  IMP_PAIR_SCORE_METHODS(NormalizedSphereDistancePairScore);
  IMP_OBJECT_METHODS(NormalizedSphereDistancePairScore);
  ;
};

//! A score on a weighted distance between the surfaces of two spheres
/** The distance between the surfaces of the two spheres is multiplied by
    the sum of a specific attribute
    \see SphereDistancePairScore
    \see XYZR
    \see DistancePairScore
 */
class IMPCOREEXPORT WeightedSphereDistancePairScore : public PairScore {
  IMP::PointerMember<UnaryFunction> f_;
  FloatKey radius_;
  FloatKey weight_;

 public:
  WeightedSphereDistancePairScore(UnaryFunction *f, FloatKey weight,
                                  FloatKey radius = FloatKey("radius"));
  virtual double evaluate_index(Model *m,
                                const ParticleIndexPair &p,
                                DerivativeAccumulator *da) const override;
  virtual ModelObjectsTemp do_get_inputs(
      Model *m, const ParticleIndexes &pis) const override;
  IMP_PAIR_SCORE_METHODS(WeightedSphereDistancePairScore);
  IMP_OBJECT_METHODS(WeightedSphereDistancePairScore);
  ;
};

typedef score_functor::SphereDistance<score_functor::HarmonicLowerBound>
    SoftSphereDistanceScore;

/** This class is equivalent to, but faster than a
    SphereDistancePairScore with a HarmonicLowerBound.
*/
IMP_FUNCTOR_DISTANCE_PAIR_SCORE(SoftSpherePairScore, SoftSphereDistanceScore,
                                (double k,
                                 std::string name = "SoftSpherePairScore%1%"),
                                (score_functor::HarmonicLowerBound(k)), );

IMPCORE_END_NAMESPACE

#endif /* IMPCORE_SPHERE_DISTANCE_PAIR_SCORE_H */