//
//  Copyright (C) 2004-2008 Greg Landrum and Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/export.h>
#ifndef __RD_ALIGN_POINTS_H__
#define __RD_ALIGN_POINTS_H__

#include <Geometry/point.h>
#include <Geometry/Transform3D.h>
#include <Numerics/Vector.h>

namespace RDNumeric {

namespace Alignments {

//! \brief Compute an optimal alignment (minimum sum of squared distance)
// between
//! two sets of points in 3D
/*!
  \param refPoints      A vector of pointers to the reference points
  \param probePoints    A vector of pointers to the points to be aligned to the
  refPoints
  \param trans          A RDGeom::Transform3D object to capture the necessary
  transformation
  \param weights        A vector of weights for each of the points
  \param reflect        Add reflection is true
  \param maxIterations  Maximum number of iterations

  \return The sum of squared distances between the points

  <b>Note</b>
  This function returns the sum of squared distance (SSR) not the RMSD
  RMSD = sqrt(SSR/numPoints)
*/
double RDKIT_ALIGNMENT_EXPORT
AlignPoints(const RDGeom::Point3DConstPtrVect &refPoints,
            const RDGeom::Point3DConstPtrVect &probePoints,
            RDGeom::Transform3D &trans, const DoubleVector *weights = 0,
            bool reflect = false, unsigned int maxIterations = 50);
}  // namespace Alignments
}  // namespace RDNumeric

#endif
