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/*! \file USRDescriptor.h

  \brief Contains the USR descriptor. Use MolDescriptors.h in client code.

*/
#include <RDGeneral/export.h>
#ifndef __RD_USR_H__
#define __RD_USR_H__

#include <Geometry/point.h>
#include <Numerics/Vector.h>

namespace RDKit {
class ROMol;
class Conformer;
namespace Descriptors {
/*!
  Calculates the ultra-fast shape recognition (USR) descriptor

  Reference: P. J. Ballester, W. G. Richards, JCC (2007), 28, 1711 - 1723.

  Derived from RDKit Python implementation of Jan Domanski
  who derived his code from Adrian Schreyer's code:
  http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default

  \param mol          the molecule of interest
  \param descriptor   storage for the computed USR descriptor
  \param confId       the conformer Id

*/
RDKIT_DESCRIPTORS_EXPORT void USR(const ROMol &mol,
                                  std::vector<double> &descriptor,
                                  int confId = -1);

/*!
  Calculates the ultra-fast shape recognition with CREDO atom types (USRCAT)
  descriptor

  Reference: A. M. Schreyer, T. Blundell, J. Cheminf. (2012), 4, 27.

  Derived from Python implementation Adrian Schreyer:
  http://hg.adrianschreyer.eu/usrcat/src/70e075d93cd2?at=default

  \param mol          the molecule of interest
  \param descriptor   storage for the computed USR descriptor
  \param confId       the conformer Id

*/
RDKIT_DESCRIPTORS_EXPORT void USRCAT(
    const ROMol &mol, std::vector<double> &descriptor,
    std::vector<std::vector<unsigned int>> &atomIds, int confId = -1);
/*!
  Calculates the four distance distributions for the USR descriptor

  \param coords      the atom coordinates
  \param dist        storage for the four distance distributions
  \param points      storage for the four points

*/
RDKIT_DESCRIPTORS_EXPORT void calcUSRDistributions(
    const RDGeom::Point3DConstPtrVect &coords,
    std::vector<std::vector<double>> &dist,
    std::vector<RDGeom::Point3D> &points);

/*!
  Calculates the four distance distributions for the USR descriptor

  \param coords      the atom coordinates
  \param points      vector with the points
  \param dist   storage for the distance distributions

*/
RDKIT_DESCRIPTORS_EXPORT void calcUSRDistributionsFromPoints(
    const RDGeom::Point3DConstPtrVect &coords,
    const std::vector<RDGeom::Point3D> &points,
    std::vector<std::vector<double>> &dist);

/*!
  Calculates the USR descriptor from the four distance distributions

  \param dist        vector with the four distance distributions
  \param descriptor  storage for the computed USR descriptor

*/
RDKIT_DESCRIPTORS_EXPORT void calcUSRFromDistributions(
    const std::vector<std::vector<double>> &dist,
    std::vector<double> &descriptor);

/*!
  Calculates the score between two USRCAT descriptors with weights

  \param d1       descriptor 1
  \param d2       descriptor 2
  \param weights  the weights for each subset of moments

  \return the score
*/
RDKIT_DESCRIPTORS_EXPORT double calcUSRScore(
    const std::vector<double> &d1, const std::vector<double> &d2,
    const std::vector<double> &weights);

}  // end of namespace Descriptors
}  // end of namespace RDKit

#endif