linear_distance_pair_scores.h

Go to the documentation of this file.

/**
 *  \file linear_distance_pair_scores.h
 *  \brief A Score on the distance between a pair of particles.
 *
 *  Copyright 2007-2021 IMP Inventors. All rights reserved.
 */

#ifndef IMPNPCTRANSPORT_LINEAR_DISTANCE_PAIR_SCORES_H
#define IMPNPCTRANSPORT_LINEAR_DISTANCE_PAIR_SCORES_H

#include "npctransport_config.h"
#include <IMP/PairScore.h>
#include <IMP/pair_macros.h>
#include <IMP/core/XYZR.h>
#include <IMP/algebra/utility.h>
#include "internal/sites.h"

#include <boost/array.hpp>

IMPNPCTRANSPORT_BEGIN_NAMESPACE

#ifndef SWIG
/**
   Evaluates a linear pair potential, such that score = k * (delta_length - x0)
   is returned.
   Also, updates the derivative vectors of the particles if da is not null.

   @param[out] d_xyzr0 pointer to derivative of particle 0
   @param[out] d_xyzr1 pointer to derivative of particle 1
   @param[in,out] da accumulator for score derivatives to be updated
   @param[in] delta a vector that represents the displacement between the
                    two particles
   @param delta_length the cached length of delta, assumed correct, and required
                       for faster calculation
   @param x0        resting distance (where score = 0)
   @param k         score linear coefficient. Note that the score is attractive
                    for a positive k, and repulsive for a negative k
                    (assuming the lower the score the better).
   @return the score
 */
inline double do_evaluate_index(algebra::Sphere3D& d_xyzr0,
                                algebra::Sphere3D& d_xyzr1,
                                DerivativeAccumulator *da,
                                const algebra::Vector3D &delta,
                                double delta_length, double x0, double k) {
  double shifted_length = delta_length - x0;
  double score = k * shifted_length;
  static const double MIN_DISTANCE = .00001;
  if (da && delta_length > MIN_DISTANCE) {
    algebra::Vector3D deriv = k * delta / delta_length;  // deriv magnitude is k
    Model::add_to_coordinate_derivatives(d_xyzr0, deriv, *da);
    Model::add_to_coordinate_derivatives(d_xyzr1, -deriv, *da);
    IMP_LOG(TERSE, "Distance: " << shifted_length << "\nscore: " << score
                                << "\nderiv: " << deriv << std::endl);
  }
  IMP_CHECK_CODE ( else {
      IMP_LOG(TERSE, "Distance: " << shifted_length << "\nscore: " << score
              << std::endl);
    } );
  return score;
}
#endif

/**
   A soft linear repulsive score between two spheres.
   If the spheres penetrate each other, the score is
   ( k_ * [penetration-magnitude] kcal/mol), otherwise the score is 0.
 */
class IMPNPCTRANSPORTEXPORT LinearSoftSpherePairScore : public PairScore {
 private:
  // score potential coefficient (larger = stronger repulsion)
  double k_;

 protected:
  //! evaluates the soft linear repulsive score, for spheres s0 and s1,
  //! outputing derivatives to ds0 and ds1 scaled by da, if da is not null
  inline double evaluate_index
    (algebra::Sphere3D const& s0,
     algebra::Sphere3D const& s1,
     algebra::Sphere3D& ds0,
     algebra::Sphere3D& ds1,
     DerivativeAccumulator *da) const;

 public:

  LinearSoftSpherePairScore(double k,
                            std::string name = "LinearSSPairScore%1%");

  virtual double evaluate_index(Model *m, const ParticleIndexPair &p,
                                DerivativeAccumulator *da) const IMP_OVERRIDE;

  virtual double evaluate_indexes(Model *m,
                                  const ParticleIndexPairs &pips,
                                  DerivativeAccumulator *da,
                                  unsigned int lower_bound,
                                  unsigned int upper_bound) const IMP_OVERRIDE;

  double evaluate_if_good_indexes
    ( Model *m,
      const ParticleIndexPairs &p,
      DerivativeAccumulator *da,
      double max, unsigned int lower_bound, unsigned int upper_bound) const
  {
    double ret = 0;
    for (unsigned int i = lower_bound; i < upper_bound; ++i) {
      ret += evaluate_if_good_index(m, p[i], da, max - ret);
      if (ret > max) return std::numeric_limits<double>::max();
    }
    return ret;
  }


  virtual ModelObjectsTemp do_get_inputs(Model *m,
                                         const ParticleIndexes &pis) const;

  //! returns the k for sphere-sphere repulsion
  double get_k() const { return k_; }

  IMP_OBJECT_METHODS(LinearSoftSpherePairScore);
  ;
};

#ifndef IMP_DOXYGEN

//! evaluates the soft linear repulsive score, for spheres s0 and s1,
//! outputing derivatives to ds0 and ds1 scaled by da, if da is not null
inline double
LinearSoftSpherePairScore::evaluate_index
(algebra::Sphere3D const& s0,
 algebra::Sphere3D const& s1,
 algebra::Sphere3D& ds0,
 algebra::Sphere3D& ds1,
 DerivativeAccumulator *da) const
{
  IMP_OBJECT_LOG;
  algebra::Vector3D delta =
      s0.get_center() - s1.get_center();
  double delta_length_2 =
      delta.get_squared_magnitude();  // (work with sqr for efficiency)
  double x0 =
      s0.get_radius() + s1.get_radius();
  double x0_2 = x0 * x0;
  bool not_penetrating = delta_length_2 > x0_2;
  if (not_penetrating) return 0;
  // penetrating spheres ; -k_ in order to get a repulsive score
  double delta_length = std::sqrt(delta_length_2);
  return do_evaluate_index(ds0, ds1, da,
                           delta, delta_length, x0, -k_);
}

// evaluates the soft linear repulsive score, using the internal Model
// indexing to access particles data (see Model/include/internal/)
inline double
LinearSoftSpherePairScore::evaluate_index
( Model *m,
  const ParticleIndexPair &pp,
  DerivativeAccumulator *da) const
{
  IMP_OBJECT_LOG;
  algebra::Sphere3D const& s0(m->get_sphere(pp[0]));
  algebra::Sphere3D const& s1(m->get_sphere(pp[1]));
  algebra::Sphere3D* d_xyzrs=
    m->access_sphere_derivatives_data();
  algebra::Sphere3D& ds0( d_xyzrs[pp[0].get_index()] );
  algebra::Sphere3D& ds1( d_xyzrs[pp[1].get_index()] );
  return evaluate_index(s0, s1, ds0, ds1,  da);
}

//! evaluate all index pairs between pis[lower_bound] and pis[upper_bound]
//! and update their coordinate derivatives scaled by da, if da is not null
inline double
LinearSoftSpherePairScore::evaluate_indexes
( Model *m,
  const ParticleIndexPairs &pips,
  DerivativeAccumulator *da,
  unsigned int lower_bound,
  unsigned int upper_bound ) const
{
  IMP_OBJECT_LOG;
  algebra::Sphere3D const* xyzrs=
      m->access_spheres_data();
  algebra::Sphere3D* d_xyzrs=
    m->access_sphere_derivatives_data();
  double ret = 0;
  for (unsigned int i = lower_bound; i < upper_bound; ++i) {
    int i0(pips[i][0].get_index());
    int i1(pips[i][1].get_index());
    ret += evaluate_index( xyzrs[i0], xyzrs[i1],
                           d_xyzrs[i0], d_xyzrs[i1],
                           da);
  }
  return ret;
}

#endif

/**
   A soft linear attractive / repulsive score between two spheres.
   The score is 0 if the spheres are beyond the attractive range.
   Within the attractive range, the score decreases linearly (= attraction)
   with slope k_attr_ until the spheres touch. Once the spheres begin to
   penetrate each other, the score rises linearly with slope k_rep_
   (= repulsion), though it may be negative for small penetration.
*/
class IMPNPCTRANSPORTEXPORT LinearInteractionPairScore : public PairScore {
#ifndef SWIG
 public:
  /** cache for reusable intermediate calculation */
  struct EvaluationCache {
    // the squared-distance between particle centers:
    double particles_delta_squared;
    // the sum of particle radii:
    double sum_particles_radii;
  };
#endif

 private:
  double range_attr_,  // range of attraction between particles
      k_rep_,          // repulsion coeficcient
      k_attr_;         // attraction coefficient

  // cache for reusable intermediate calcualtions of evaluate_infex
  mutable EvaluationCache cache_;

 protected:
  //! evaluates the linear interaction score, for spheres s0 and s1,
  //! outputing derivatives to ds0 and ds1 scaled by da, if da is not null
  inline double evaluate_index
    (algebra::Sphere3D const& s0,
     algebra::Sphere3D const& s1,
     algebra::Sphere3D& ds0,
     algebra::Sphere3D& ds1,
     DerivativeAccumulator *da) const;

 public:
  /**
   The score is 0 if the spheres are beyond the attractive range.
   Within the attractive range, the score decreases linearly (= attraction)
   with slope k_attr_ until the spheres touch. Once the spheres begin to
   penetrate each other, the score rises linearly with slope k_rep_
   (= repulsion), though it may be negative for small penetration.

   The energy potential difference between the unbound state and when the
   beads touch is:
     DELTA-U=0.5*k_attr*range_attr [kcal/mol]

     @param k_rep repulsion force constant in kcal/mol/A units
     @param range_attr attraction range between sphere surfaces
     @param k_attr attraction force constant in kcal/mol/A unit
     @param name score object names
   */
  LinearInteractionPairScore(double k_rep, double range_attr, double k_attr,
                             std::string name = "LinearIDPairScore%1%");

#ifndef SWIG
  // returns cached intermediate computations from last call to
  // this->evaluate_index()
  EvaluationCache const &get_evaluation_cache() const { return cache_; }
#endif

  IMP_IMPLEMENT(double evaluate_index(Model *m, const ParticleIndexPair &p,
                                      DerivativeAccumulator *da) const
                IMP_OVERRIDE);
  IMP_IMPLEMENT_INLINE(double evaluate_if_good_index
                       ( Model *m,
                         const ParticleIndexPair &p,
                         DerivativeAccumulator *da,
                         double max ) const,
                       {
                         IMP_UNUSED(max);
                         return evaluate_index(m, p, da);
                       }
                       );

  //! evaluate all index pairs between pips[lower_bound] and pis[upper_bound]
  //! and update their coordinate derivatives scaled by da, if da is not null
  virtual double evaluate_indexes(Model *m,
                                  const ParticleIndexPairs &pips,
                                  DerivativeAccumulator *da,
                                  unsigned int lower_bound,
                                  unsigned int upper_bound) const IMP_OVERRIDE;

  double evaluate_if_good_index(Model *m, const ParticleIndexPairs &p,
                                DerivativeAccumulator *da, double max,
                                unsigned int lower_bound,
                                unsigned int upper_bound) const {
    double ret = 0;
    for (unsigned int i = lower_bound; i < upper_bound; ++i) {
      ret += evaluate_if_good_index(m, p[i], da, max - ret);
      if (ret > max) return std::numeric_limits<double>::max();
    }
    return ret;
  }

  ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const
      IMP_OVERRIDE;

  //! returns the range for sphere-sphere attraction in A
  double get_range_attraction() const { return range_attr_; }

  //! returns the k for sphere-sphere attraction in kcal/mol/A units
  double get_k_attraction() const { return k_attr_; }

  //! set k for sphere-sphere attraction in kcal/mol/A units
  void set_k_attraction(double k_attr) {
    k_attr_= k_attr;
  }

  //! returns the k for sphere-sphere repulsion in kcal/mol/A units
  double get_k_repulsion() const { return k_rep_; }

  //! set k for sphere-sphere repulsion in kcal/mol/A units
  void set_k_repulsion(double k_rep) {
    k_rep_ = k_rep;
  }

  IMP_OBJECT_METHODS(LinearInteractionPairScore);
};

#ifndef IMP_DOXYGEN

//! evaluates the linear interaction score, for spheres s0 and s1,
//! outputing derivatives to ds0 and ds1 scaled by da, if da is not null
inline double
LinearInteractionPairScore::evaluate_index
(algebra::Sphere3D const& s0,
 algebra::Sphere3D const& s1,
 algebra::Sphere3D& ds0,
 algebra::Sphere3D& ds1,
 DerivativeAccumulator *da) const
{
   // Associate intermediate variables with cache_, for further reuse:
  double &delta_length_2 = cache_.particles_delta_squared;
  double &x0 = cache_.sum_particles_radii;
  algebra::Vector3D delta =
      s0.get_center() - s1.get_center();
  delta_length_2 = delta.get_squared_magnitude();
  IMP_LOG(PROGRESS,
          "LinearInteractionPairScore cached delta2 "
          << cache_.particles_delta_squared << std::endl);
  x0 = s0.get_radius() + s1.get_radius();
  // Terminate immediately if very far, work with squares for speed
  // equivalent to [delta_length > x0 + attr_range]:
  if (delta_length_2 > std::pow(x0 + range_attr_, 2)) return 0;
  double offset = -range_attr_ * k_attr_;
  double delta_length = std::sqrt(delta_length_2);
  if (delta_length > x0) {  // attractive regime
    return  // decreases with slope k_attr_ as spheres get closer
      (do_evaluate_index(ds0, ds1, da,
                         delta, delta_length, x0, k_attr_) +
         offset);
  } else {  // repulsive regime, may be negative for small penetration
    return (do_evaluate_index(ds0, ds1, da,
                              delta, delta_length, x0, -k_rep_) +
            offset);
  }
}

inline double
LinearInteractionPairScore::evaluate_index
( Model *m,
  const ParticleIndexPair &pp,
  DerivativeAccumulator *da) const
{
  IMP_OBJECT_LOG;
  algebra::Sphere3D const& s0(m->get_sphere(pp[0]));
  algebra::Sphere3D const& s1(m->get_sphere(pp[1]));
  algebra::Sphere3D* d_xyzrs=
    m->access_sphere_derivatives_data();
  algebra::Sphere3D& ds0( d_xyzrs[pp[0].get_index()] );
  algebra::Sphere3D& ds1( d_xyzrs[pp[1].get_index()] );
  return evaluate_index(s0, s1, ds0, ds1, da);
 }

inline double
LinearInteractionPairScore::evaluate_indexes
( Model *m,
  const ParticleIndexPairs &pips,
  DerivativeAccumulator *da,
  unsigned int lower_bound,
  unsigned int upper_bound) const
{
  IMP_OBJECT_LOG;
  algebra::Sphere3D const* xyzrs=
      m->access_spheres_data();
  algebra::Sphere3D* d_xyzrs=
    m->access_sphere_derivatives_data();
  double ret = 0;
  for (unsigned int i = lower_bound; i < upper_bound; ++i) {
    int i0(pips[i][0].get_index());
    int i1(pips[i][1].get_index());
    ret += evaluate_index( xyzrs[i0], xyzrs[i1],
                           d_xyzrs[i0], d_xyzrs[i1],
                           da);
  }
  return ret;
}


#endif

/**
   A soft linear attractive / repulsive score between two spheres
   for the backbone of a chain.
*/
class IMPNPCTRANSPORTEXPORT LinearWellPairScore : public PairScore {
 private:
  double rest_length_factor_, k_;

 public:
  /**
     a linear well pair potential that keeps two particles around
     a resting distance relative to their radii

     @param rest_length_factor the resting distance between particles
                               relative to their sum of radii
     @param k the force constant (attractive if beyond or repulsive
              if below rest length) in units kcal/mol/A
     @param name the name of the score
   */
  LinearWellPairScore(double rest_length_factor, double k,
                      std::string name = "LinearIDPairScore%1%");

  void set_rest_length_factor(double rest_length_factor)
  { rest_length_factor_ = rest_length_factor; }
  double get_rest_length_factor() const { return rest_length_factor_; }
  void set_k(double k)
  { k_ = k; }
  double get_k() { return k_; }
  double evaluate_index(Model *m, const ParticleIndexPair &p,
                        DerivativeAccumulator *da) const IMP_OVERRIDE;
  ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const;
  IMP_PAIR_SCORE_METHODS(LinearWellPairScore);
  IMP_OBJECT_METHODS(LinearWellPairScore);
  ;
};

#ifndef IMP_DOXYGEN
inline double
LinearWellPairScore::evaluate_index
( Model *m,
  const ParticleIndexPair &pp,
  DerivativeAccumulator *da) const
{
  IMP_OBJECT_LOG;
  algebra::Sphere3D const& s0 = m->get_sphere(pp[0]);
  algebra::Sphere3D const& s1 = m->get_sphere(pp[1]);
    algebra::Sphere3D* d_xyzrs=
    m->access_sphere_derivatives_data();
  algebra::Sphere3D& ds0( d_xyzrs[pp[0].get_index()] );
  algebra::Sphere3D& ds1( d_xyzrs[pp[1].get_index()] );
  double x0 = (s0.get_radius() + s1.get_radius()) * rest_length_factor_;
  algebra::Vector3D delta = s0.get_center() - s1.get_center();
  double delta_length_2 = delta.get_squared_magnitude();
  double delta_length = std::sqrt(delta_length_2);
  if (delta_length > x0) {  // attractive regime
    return  // k_ > 0 = get spheres closer
      do_evaluate_index(ds0, ds1, da,
                        delta, delta_length, x0, k_);
  } else {
    return// -k_ < 0 = keep spheres apart
      do_evaluate_index(ds0, ds1, da,
                        delta, delta_length, x0, -k_);
  }
}
#endif

IMP_OBJECTS(LinearWellPairScore, LinearWellPairScores);


IMPNPCTRANSPORT_END_NAMESPACE

#endif /* IMPNPCTRANSPORT_LINEAR_DISTANCE_PAIR_SCORES_H */