// $Id$
//
//  Copyright (C) 2013 Paolo Tosco
//
//  Copyright (C) 2004-2006 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 "TorsionAngle.h"
#include "Params.h"
#include <cmath>
#include <ForceField/ForceField.h>
#include <RDGeneral/Invariant.h>

namespace ForceFields {
namespace MMFF {
namespace Utils {
double calcTorsionCosPhi(const RDGeom::Point3D &iPoint,
                         const RDGeom::Point3D &jPoint,
                         const RDGeom::Point3D &kPoint,
                         const RDGeom::Point3D &lPoint) {
  RDGeom::Point3D r1 = iPoint - jPoint;
  RDGeom::Point3D r2 = kPoint - jPoint;
  RDGeom::Point3D r3 = jPoint - kPoint;
  RDGeom::Point3D r4 = lPoint - kPoint;
  RDGeom::Point3D t1 = r1.crossProduct(r2);
  RDGeom::Point3D t2 = r3.crossProduct(r4);
  double cosPhi = t1.dotProduct(t2) / (t1.length() * t2.length());
  clipToOne(cosPhi);

  return cosPhi;
}

boost::tuple<double, double, double> calcTorsionForceConstant(
    const MMFFTor *mmffTorParams) {
  return boost::make_tuple(mmffTorParams->V1, mmffTorParams->V2,
                           mmffTorParams->V3);
}

double calcTorsionEnergy(const double V1, const double V2, const double V3,
                         const double cosPhi) {
  double cos2Phi = 2.0 * cosPhi * cosPhi - 1.0;
  double cos3Phi = cosPhi * (2.0 * cos2Phi - 1.0);

  return (0.5 *
          (V1 * (1.0 + cosPhi) + V2 * (1.0 - cos2Phi) + V3 * (1.0 + cos3Phi)));
}

void calcTorsionGrad(RDGeom::Point3D *r, RDGeom::Point3D *t, double *d,
                     double **g, double &sinTerm, double &cosPhi) {
  // -------
  // dTheta/dx is trickier:
  double dCos_dT[6] = {1.0 / d[0] * (t[1].x - cosPhi * t[0].x),
                       1.0 / d[0] * (t[1].y - cosPhi * t[0].y),
                       1.0 / d[0] * (t[1].z - cosPhi * t[0].z),
                       1.0 / d[1] * (t[0].x - cosPhi * t[1].x),
                       1.0 / d[1] * (t[0].y - cosPhi * t[1].y),
                       1.0 / d[1] * (t[0].z - cosPhi * t[1].z)};

  g[0][0] += sinTerm * (dCos_dT[2] * r[1].y - dCos_dT[1] * r[1].z);
  g[0][1] += sinTerm * (dCos_dT[0] * r[1].z - dCos_dT[2] * r[1].x);
  g[0][2] += sinTerm * (dCos_dT[1] * r[1].x - dCos_dT[0] * r[1].y);

  g[1][0] += sinTerm *
             (dCos_dT[1] * (r[1].z - r[0].z) + dCos_dT[2] * (r[0].y - r[1].y) +
              dCos_dT[4] * (-r[3].z) + dCos_dT[5] * (r[3].y));
  g[1][1] += sinTerm *
             (dCos_dT[0] * (r[0].z - r[1].z) + dCos_dT[2] * (r[1].x - r[0].x) +
              dCos_dT[3] * (r[3].z) + dCos_dT[5] * (-r[3].x));
  g[1][2] += sinTerm *
             (dCos_dT[0] * (r[1].y - r[0].y) + dCos_dT[1] * (r[0].x - r[1].x) +
              dCos_dT[3] * (-r[3].y) + dCos_dT[4] * (r[3].x));

  g[2][0] += sinTerm *
             (dCos_dT[1] * (r[0].z) + dCos_dT[2] * (-r[0].y) +
              dCos_dT[4] * (r[3].z - r[2].z) + dCos_dT[5] * (r[2].y - r[3].y));
  g[2][1] += sinTerm *
             (dCos_dT[0] * (-r[0].z) + dCos_dT[2] * (r[0].x) +
              dCos_dT[3] * (r[2].z - r[3].z) + dCos_dT[5] * (r[3].x - r[2].x));
  g[2][2] += sinTerm *
             (dCos_dT[0] * (r[0].y) + dCos_dT[1] * (-r[0].x) +
              dCos_dT[3] * (r[3].y - r[2].y) + dCos_dT[4] * (r[2].x - r[3].x));

  g[3][0] += sinTerm * (dCos_dT[4] * r[2].z - dCos_dT[5] * r[2].y);
  g[3][1] += sinTerm * (dCos_dT[5] * r[2].x - dCos_dT[3] * r[2].z);
  g[3][2] += sinTerm * (dCos_dT[3] * r[2].y - dCos_dT[4] * r[2].x);
}
}

TorsionAngleContrib::TorsionAngleContrib(ForceField *owner, unsigned int idx1,
                                         unsigned int idx2, unsigned int idx3,
                                         unsigned int idx4,
                                         const MMFFTor *mmffTorParams) {
  PRECONDITION(owner, "bad owner");
  PRECONDITION((idx1 != idx2) && (idx1 != idx3) && (idx1 != idx4) &&
                   (idx2 != idx3) && (idx2 != idx4) && (idx3 != idx4),
               "degenerate points");
  URANGE_CHECK(idx1, owner->positions().size());
  URANGE_CHECK(idx2, owner->positions().size());
  URANGE_CHECK(idx3, owner->positions().size());
  URANGE_CHECK(idx4, owner->positions().size());

  dp_forceField = owner;
  d_at1Idx = idx1;
  d_at2Idx = idx2;
  d_at3Idx = idx3;
  d_at4Idx = idx4;
  d_V1 = mmffTorParams->V1;
  d_V2 = mmffTorParams->V2;
  d_V3 = mmffTorParams->V3;
}

double TorsionAngleContrib::getEnergy(double *pos) const {
  PRECONDITION(dp_forceField, "no owner");
  PRECONDITION(pos, "bad vector");

  RDGeom::Point3D iPoint(pos[3 * d_at1Idx], pos[3 * d_at1Idx + 1],
                         pos[3 * d_at1Idx + 2]);
  RDGeom::Point3D jPoint(pos[3 * d_at2Idx], pos[3 * d_at2Idx + 1],
                         pos[3 * d_at2Idx + 2]);
  RDGeom::Point3D kPoint(pos[3 * d_at3Idx], pos[3 * d_at3Idx + 1],
                         pos[3 * d_at3Idx + 2]);
  RDGeom::Point3D lPoint(pos[3 * d_at4Idx], pos[3 * d_at4Idx + 1],
                         pos[3 * d_at4Idx + 2]);

  return Utils::calcTorsionEnergy(
      d_V1, d_V2, d_V3,
      Utils::calcTorsionCosPhi(iPoint, jPoint, kPoint, lPoint));
}

void TorsionAngleContrib::getGrad(double *pos, double *grad) const {
  PRECONDITION(dp_forceField, "no owner");
  PRECONDITION(pos, "bad vector");
  PRECONDITION(grad, "bad vector");

  double *g[4] = {&(grad[3 * d_at1Idx]), &(grad[3 * d_at2Idx]),
                  &(grad[3 * d_at3Idx]), &(grad[3 * d_at4Idx])};

  RDGeom::Point3D r[4];
  RDGeom::Point3D t[2];
  double d[2];
  double cosPhi;
  RDKit::ForceFieldsHelper::computeDihedral(
      pos, d_at1Idx, d_at2Idx, d_at3Idx, d_at4Idx, nullptr, &cosPhi, r, t, d);
  double sinPhiSq = 1.0 - cosPhi * cosPhi;
  double sinPhi = ((sinPhiSq > 0.0) ? sqrt(sinPhiSq) : 0.0);
  double sin2Phi = 2.0 * sinPhi * cosPhi;
  double sin3Phi = 3.0 * sinPhi - 4.0 * sinPhi * sinPhiSq;
  // dE/dPhi is independent of cartesians:
  double dE_dPhi =
      0.5 * (-(d_V1)*sinPhi + 2.0 * d_V2 * sin2Phi - 3.0 * d_V3 * sin3Phi);
#if 0
      if(dE_dPhi!=dE_dPhi){
        std::cout << "\tNaN in Torsion("<<d_at1Idx<<","<<d_at2Idx<<","<<d_at3Idx<<","<<d_at4Idx<<")"<< std::endl;
        std::cout << "sin: " << sinPhi << std::endl;
        std::cout << "cos: " << cosPhi << std::endl;
      }

#endif
  // FIX: use a tolerance here
  // this is hacky, but it's per the
  // recommendation from Niketic and Rasmussen:
  double sinTerm =
      -dE_dPhi * (isDoubleZero(sinPhi) ? (1.0 / cosPhi) : (1.0 / sinPhi));

  Utils::calcTorsionGrad(r, t, d, g, sinTerm, cosPhi);
}
}
}
