atom/distance.h

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/**
 *  \file IMP/atom/distance.h
 *  \brief distance metrics
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPATOM_DISTANCE_H
#define IMPATOM_DISTANCE_H

#include <IMP/atom/atom_config.h>
#include <IMP/core/XYZ.h>
#include "Hierarchy.h"
#include "Selection.h"
#include <IMP/algebra/distance.h>
#include "IMP/base_types.h"

IMPATOM_BEGIN_NAMESPACE
/**
   Get the rmsd between two lists of particles
 */
IMPATOMEXPORT double get_rmsd_transforming_first(
    const IMP::algebra::Transformation3D& tr, const core::XYZs& s0,
    const core::XYZs& s1);

/**
   Get the rmsd between two lists of particles
 */
IMPATOMEXPORT double get_rmsd(const core::XYZs& s0, const core::XYZs& s1);

/** RMSD on a pair of Selections.*/
IMPATOMEXPORT double get_rmsd(const Selection& s0, const Selection& s1);

/** RMSD on a pair of Selections.*/
IMPATOMEXPORT double get_rmsd_transforming_first(
    const algebra::Transformation3D& tr, const Selection& s0,
    const Selection& s1);

//! Calculate distance the root mean square deviation between two sets of 3D points.
/**
   \note the function assumes correspondence between the two sets of
   points and does not need rigid alignment. Note that it is different from
   get_drms().

   \genericgeometry
 */
template <class Vector3DsOrXYZs0, class Vector3DsOrXYZs1>
inline double get_drmsd(const Vector3DsOrXYZs0& m0,
                        const Vector3DsOrXYZs1& m1) {
  using algebra::get_vector_geometry;
  IMP_USAGE_CHECK(m0.size() == m1.size(), "The input sets of XYZ points "
                                              << "should be of the same size");
  double drmsd = 0.0;

  int npairs = 0;
  for (unsigned i = 0; i < m0.size() - 1; ++i) {
    algebra::Vector3D v0i = get_vector_geometry(m0[i]);
    algebra::Vector3D v1i = get_vector_geometry(m1[i]);

    for (unsigned j = i + 1; j < m0.size(); ++j) {
      algebra::Vector3D v0j = get_vector_geometry(m0[j]);
      algebra::Vector3D v1j = get_vector_geometry(m1[j]);

      double dist0 = algebra::get_distance(v0i, v0j);
      double dist1 = algebra::get_distance(v1i, v1j);
      drmsd += (dist0 - dist1) * (dist0 - dist1);
      npairs++;
    }
  }
  return std::sqrt(drmsd / npairs);
}


//! Calculate the distance root mean square deviation between two sets of 3D points
//! with a distance threshold
/**
   \note the function assumes correspondence between the two sets of
   points and does not need rigid alignment. Note that it is different from
   get_drmsd().

   \genericgeometry
 */
template <class Vector3DsOrXYZs0, class Vector3DsOrXYZs1>
inline double get_drmsd_Q(const Vector3DsOrXYZs0& m0,
                          const Vector3DsOrXYZs1& m1, double threshold) {
  using algebra::get_vector_geometry;
  IMP_USAGE_CHECK(m0.size() == m1.size(), "The input sets of XYZ points "
                                              << "should be of the same size");
  double drmsd = 0.0;

  int npairs = 0;
  for (unsigned i = 0; i < m0.size() - 1; ++i) {
    algebra::Vector3D v0i = get_vector_geometry(m0[i]);
    algebra::Vector3D v1i = get_vector_geometry(m1[i]);

    for (unsigned j = i + 1; j < m0.size(); ++j) {
      algebra::Vector3D v0j = get_vector_geometry(m0[j]);
      algebra::Vector3D v1j = get_vector_geometry(m1[j]);

      double dist0 = algebra::get_distance(v0i, v0j);
      double dist1 = algebra::get_distance(v1i, v1j);
      if (dist0<=threshold || dist1<=threshold){
        drmsd += (dist0 - dist1) * (dist0 - dist1);
        npairs++;
      }
    }
  }
  return std::sqrt(drmsd / npairs);
}


//! Computes the native overlap between two sets of 3D points
/**
  \param[in] m1 first set
  \param[in] m2 second set
  \param[in] threshold threshold distance (angstroms) for the calculation
  \note the function assumes correspondence between two sets of points and does
  not perform rigid alignment.
  \return the native overlap, as a percentage (from 0 to 100)
  \genericgeometry
**/
template <class Vector3DsOrXYZs0, class Vector3DsOrXYZs1>
inline double get_native_overlap(const Vector3DsOrXYZs0& m1,
                                 const Vector3DsOrXYZs1& m2, double threshold) {
  IMP_USAGE_CHECK(m1.size() == m2.size(),
                  "native_overlap: The input sets of XYZ points "
                      << "should be of the same size");
  unsigned int distances = 0;
  for (unsigned int i = 0; i < m1.size(); i++) {
    double d = algebra::get_distance(get_vector_geometry(m1[i]),
                                     get_vector_geometry(m2[i]));
    if (d <= threshold) distances++;
  }
  return 100.0 * distances / m1.size();
}

/*! Distance-RMS between two sets of points, defined as:
    sqrt( sum[ (d1ij**2 - d2ij**2)**2]/(4 * sum[d1ij**2]) )
    (Levitt, 1992)
    d1ij - distance between points i and j in set m1 (the "reference" set)
    d2ij - distance between points i and j in set m2
  \param[in] m1 set of points
  \param[in] m2 set of points
*/
template <class Vector3DsOrXYZs0, class Vector3DsOrXYZs1>
inline double get_drms(const Vector3DsOrXYZs0& m1, const Vector3DsOrXYZs1& m2) {
  IMP_USAGE_CHECK(m1.size() == m2.size(),
                  "native_overlap: The input sets of XYZ points "
                      << "should be of the same size");

  unsigned int n = m1.size();
  double drms = 0.0;
  double sum_d1ij = 0.0;
  for (unsigned int i = 0; i < n; ++i) {
    for (unsigned int j = i + 1; j < n; ++j) {
      double sqd1 = algebra::get_squared_distance(get_vector_geometry(m1[i]),
                                                  get_vector_geometry(m1[j]));
      double sqd2 = algebra::get_squared_distance(get_vector_geometry(m2[i]),
                                                  get_vector_geometry(m2[j]));
      drms += (sqd1 - sqd2) * (sqd1 - sqd2);
      sum_d1ij += sqd1;
    }
  }
  drms /= (4 * sum_d1ij);
  return sqrt(drms);
}

//! DRMS between two sets of rigid bodies.
/** Points ij belonging to the same rigid body are not evaluated, as
    they are the same in both sets
  \param[in] m1 set of points
  \param[in] m2 set of points
  \param[in] ranges of points considered to be the same rigid body. Eg,
        (0-29,30-49) means two rigid bodies, first with the 30 first atoms,
        second with the last 20
*/
template <class Vector3DsOrXYZs0, class Vector3DsOrXYZs1>
inline double get_rigid_bodies_drms(const Vector3DsOrXYZs0& m1,
                                    const Vector3DsOrXYZs1& m2,
                                    const IMP::IntRanges& ranges) {
  IMP_USAGE_CHECK(m1.size() == m2.size(),
                  "get_rigid_bodies_drms: The input sets of XYZ points "
                      << "should be of the same size");
  int n = m1.size();
  int rn = ranges.size();
  double drms = 0.0;
  double sum_d1ij = 0.0;
  for (int i = 0; i < n; ++i) {
    int range1 = -1;
    for (int k = 0; k < rn; ++k) {
      if (i >= ranges[k].first && i <= ranges[k].second) {
        range1 = k;
        break;
      }
    }
    IMP_USAGE_CHECK(range1 >= 0, "Point " << i << " of m1 does not belong to "
                                                  "any range");
    for (int j = i + 1; j < n; ++j) {
      int range2 = -1;
      for (int k = 0; k < rn; ++k) {
        if (j >= ranges[k].first && j <= ranges[k].second) {
          range2 = k;
          break;
        }
      }
      IMP_USAGE_CHECK(range2 >= 0, "Point " << j << " of m2 does not belong to "
                                                    "any range");

      double sqd1 = algebra::get_squared_distance(get_vector_geometry(m1[i]),
                                                  get_vector_geometry(m1[j]));
      sum_d1ij += sqd1;
      if (range1 != range2) {
        // points i and j in different ranges compare distances
        double sqd2 = algebra::get_squared_distance(get_vector_geometry(m2[i]),
                                                    get_vector_geometry(m2[j]));
        drms += (sqd1 - sqd2) * (sqd1 - sqd2);
      }
    }
  }
  drms /= (4 * sum_d1ij);
  return sqrt(drms);
}

//! Measure the difference between two placements of the same set of points
/**
   \param[in] source The reference placement represented by XYZ coordinates
   \param[in] target The modeled placement represented by XYZ coordinates
   \note The measure quantifies the difference between placements
   of the same structure. A rigid transformation that brings mdl1 to
   ref1 is reported.
   \return (d,a), A transformation from mdl to ref represented by
   a a distance (d) and an angle (a).
   d is the distance between the centroids of the two
   placements and a is the axis angle of the rotation matrix between
   the two placements
   \note see Lasker,Topf et al JMB, 2009 for details
 */
IMPATOMEXPORT FloatPair
    get_placement_score(const core::XYZs& source, const core::XYZs& target);

//! Measure the difference between two placements of the same set of points
/**
\param[in] ref1 The reference placement of the first component represented
               by XYZ coordinates
\param[in] ref2 The reference placement of the second component represented
               by XYZ coordinates
\param[in] mdl1 The modeled placement of the first component
           represented by XYZ coordinates
\param[in] mdl2 The modeled placement of the second component
           represented by XYZ coordinates
\return the function returns (distance score,angle score)
\note The measure quantifies the difference between the relative placements
      of two components compared to a reference relative placement.
      First, the two compared structures are brought into
      the same frame of reference by superposing the first pair of
      equivalent domains (ref1 and mdl1). Next, the distance and angle
      scores are calculated for the second component using placement_score.
\note see Topf, Lasker et al Structure, 2008 for details
 */
IMPATOMEXPORT FloatPair get_component_placement_score(const core::XYZs& ref1,
                                                      const core::XYZs& ref2,
                                                      const core::XYZs& mdl1,
                                                      const core::XYZs& mdl2);

//! Measure the RMSD between two placements of the same set of points
/**
\param[in] ref1 The reference placement of the first component represented
               by XYZ coordinates
\param[in] ref2 The reference placement of the second component represented
               by XYZ coordinates
\param[in] mdl1 The modeled placement of the first component
           represented by XYZ coordinates
\param[in] mdl2 The modeled placement of the second component
           represented by XYZ coordinates
\note The measure quantifies the RMSD between the relative placements
      of two components compared to a reference relative placement.
      First, the two compared structures are brought into
      the same frame of reference by superposing the first pair of
      equivalent domains (ref1 and mdl1). Next, the RMSD is calculated
      for the second component
\note see Lasker et al JMB, 2009 for details
 */
IMPATOMEXPORT
double get_pairwise_rmsd_score
(const core::XYZs& ref1,
 const core::XYZs& ref2,
 const core::XYZs& mdl1,
 const core::XYZs& mdl2);

/** Compute the radius of gyration $R_g$ of a set of particles. It is assumed
    the particles has coordinates (XYZ decorator), and optionally, the $R_g$
    may be weighted by mass or radius^3.

    @param ps the particles
    @param weighted If true then $R_g$ is weighted by either mass or radius^3,
       in this order of preference. If none exists, an unweighted $R_g$ is
       computed. If weighted is true, then it is is assumed that either
       all particles have mass/radius or none of them do.

    @return the weighted or unweighted radius of gyration of ps
*/
IMPATOMEXPORT
double get_radius_of_gyration
(const ParticlesTemp& ps,
 bool weighted=true);

IMPATOM_END_NAMESPACE

#endif /* IMPATOM_DISTANCE_H */