// $Id$
//
// 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/test.h>
#include <iostream>
#include <iomanip>
#include <cmath>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/utils.h>
#include <Geometry/point.h>

#include <ForceField/ForceField.h>
#include <ForceField/UFF/Params.h>
#include <ForceField/UFF/BondStretch.h>
#include <ForceField/UFF/AngleBend.h>
#include <ForceField/UFF/Nonbonded.h>
#include <ForceField/UFF/TorsionAngle.h>
#include <ForceField/UFF/DistanceConstraint.h>
#include <ForceField/UFF/AngleConstraint.h>
#include <ForceField/UFF/TorsionConstraint.h>
#include <ForceField/UFF/PositionConstraint.h>

#include <GraphMol/Atom.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/ForceFieldHelpers/UFF/Builder.h>
#include <GraphMol/MolTransforms/MolTransforms.h>

using namespace RDGeom;

void test1() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for force field basics." << std::endl;

  ForceFields::ForceField ff;
  TEST_ASSERT(ff.dimension() == 3);

  Point3D p1(0, 0, 0), p2(1, 0, 0), p3(2, 0, 0), p4(0, 1, 0);
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);
  ps.push_back(&p4);

#if 0
  Point3D f1,f2,f3,f4;
  RDGeom::PointPtrVect &fs=ff.forces();
  fs.push_back(&f1);
  fs.push_back(&f2);
  fs.push_back(&f3);
  fs.push_back(&f4);
#endif
  TEST_ASSERT(ff.positions().size() == 4);
  // TEST_ASSERT(ff.forces().size()==4);

  ff.initialize();

  TEST_ASSERT(RDKit::feq(ff.distance(0, 1), 1.0));
  TEST_ASSERT(RDKit::feq(ff.distance(1, 0), 1.0));
  TEST_ASSERT(RDKit::feq(ff.distance(0, 0), 0.0));
  TEST_ASSERT(RDKit::feq(ff.distance(0, 2), 2.0));
  TEST_ASSERT(RDKit::feq(ff.distance(2, 0), 2.0));
  TEST_ASSERT(RDKit::feq(ff.distance(0, 3), 1.0));
  TEST_ASSERT(RDKit::feq(ff.distance(3, 0), 1.0));
  TEST_ASSERT(RDKit::feq(ff.distance(3, 3), 0.0));
  TEST_ASSERT(RDKit::feq(ff.distance(1, 2), 1.0));
  TEST_ASSERT(RDKit::feq(ff.distance(2, 1), 1.0));

  std::cerr << "  done" << std::endl;
}

void testUFF1() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for basics of UFF bond-stretch terms." << std::endl;

  ForceFields::UFF::AtomicParams p1, p2;
  double restLen, forceConstant;

  // sp3 carbon:
  p1.r1 = .757;
  p1.Z1 = 1.912;
  p1.GMP_Xi = 5.343;

  // sp3 - sp3: checks basics
  restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p1, &p1);
  TEST_ASSERT(RDKit::feq(restLen, 1.514));

  forceConstant =
      ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p1, &p1);
  TEST_ASSERT(RDKit::feq(forceConstant, 699.5918));

  // sp2 carbon:
  p2.r1 = .732;
  p2.Z1 = 1.912;
  p2.GMP_Xi = 5.343;
  // sp2 - sp2: checks rBO
  restLen = ForceFields::UFF::Utils::calcBondRestLength(2.0, &p2, &p2);
  TEST_ASSERT(RDKit::feq(restLen, 1.32883, 1e-5));

  forceConstant =
      ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p2, &p2);
  TEST_ASSERT(RDKit::feq(forceConstant, 1034.69, 1e-2));

  // sp3 nitrogen:
  p2.r1 = .700;
  p2.Z1 = 2.544;
  p2.GMP_Xi = 6.899;

  // Csp3 - Nsp3: checks rEN
  restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p1, &p2);
  TEST_ASSERT(RDKit::feq(restLen, 1.451071, 1e-5));

  forceConstant =
      ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p1, &p2);
  TEST_ASSERT(RDKit::feq(forceConstant, 1057.27, 1e-2));

  // amide bond: check we can reproduce values from the UFF paper:
  // C_R:
  p1.r1 = .729;
  p1.Z1 = 1.912;
  p1.GMP_Xi = 5.343;
  // N_R:
  p2.r1 = .699;
  p2.Z1 = 2.544;
  p2.GMP_Xi = 6.899;

  restLen = ForceFields::UFF::Utils::calcBondRestLength(
      ForceFields::UFF::Params::amideBondOrder, &p1, &p2);
  TEST_ASSERT(RDKit::feq(restLen, 1.357, 1e-3));  // NOTE: the paper has 1.366

  forceConstant =
      ForceFields::UFF::Utils::calcBondForceConstant(restLen, &p1, &p2);
  TEST_ASSERT(RDKit::feq(forceConstant, 1293., 1));  // NOTE: the paper has 1293

  std::cerr << "  done" << std::endl;
}

void testUFF2() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for UFF bond-stretch terms." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1(0, 0, 0), p2(1.514, 0, 0);
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);

  ForceFields::UFF::AtomicParams param1;
  // sp3 carbon:
  param1.r1 = .757;
  param1.Z1 = 1.912;
  param1.GMP_Xi = 5.343;

  // C_3 - C_3, r0=1.514, k01=699.5918
  ForceFields::ForceFieldContrib *bs;
  bs = new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 1, &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(bs));
  ff.initialize();

  double *p, *g;
  p = new double[6];
  g = new double[6];
  for (int i = 0; i < 6; i++) {
    p[i] = 0.0;
    g[i] = 0.0;
  }

  double E;
  // edge case: zero bond length:
  E = bs->getEnergy(p);
  TEST_ASSERT(E > 0.0);
  bs->getGrad(p, g);
  for (int i = 0; i < 6; i++) {
    TEST_ASSERT(fabs(g[i]) > 0.0);
  }

  p[0] = 0;
  p[3] = 1.514;
  for (int i = 0; i < 6; i++) {
    g[i] = 0.0;
  }
  ff.initialize();
  E = bs->getEnergy(p);
  TEST_ASSERT(RDKit::feq(E, 0.0));
  bs->getGrad(p, g);
  for (int i = 0; i < 6; i++) {
    TEST_ASSERT(RDKit::feq(g[i], 0.0));
  }

  (*ff.positions()[1])[0] = 1.814;
  p[3] = 1.814;
  ff.initialize();
  E = bs->getEnergy(p);
  TEST_ASSERT(RDKit::feq(E, 31.4816));
  bs->getGrad(p, g);
  TEST_ASSERT(RDKit::feq(g[0], -209.8775));
  TEST_ASSERT(RDKit::feq(g[3], 209.8775));
  TEST_ASSERT(RDKit::feq(g[1], 0.0));
  TEST_ASSERT(RDKit::feq(g[2], 0.0));
  TEST_ASSERT(RDKit::feq(g[4], 0.0));
  TEST_ASSERT(RDKit::feq(g[5], 0.0));

  // try a different axis:
  for (int i = 0; i < 6; i++) {
    g[i] = 0.0;
    p[i] = 0.0;
  }
  ff.initialize();
  (*ff.positions()[1])[0] = 0.0;
  (*ff.positions()[1])[2] = 1.814;
  p[5] = 1.814;
  E = bs->getEnergy(p);
  TEST_ASSERT(RDKit::feq(E, 31.4816));
  bs->getGrad(p, g);
  TEST_ASSERT(RDKit::feq(g[2], -209.8775));
  TEST_ASSERT(RDKit::feq(g[5], 209.8775));
  TEST_ASSERT(RDKit::feq(g[0], 0.0));
  TEST_ASSERT(RDKit::feq(g[1], 0.0));
  TEST_ASSERT(RDKit::feq(g[3], 0.0));
  TEST_ASSERT(RDKit::feq(g[4], 0.0));

  // try a bit of minimization
  RDGeom::Point3D d;
  ff.initialize();
  (*ff.positions()[1])[2] = 0.0;
  (*ff.positions()[1])[0] = 1.814;
  ff.minimize(10, 1e-8);
  d = *(RDGeom::Point3D *)ff.positions()[0] -
      *(RDGeom::Point3D *)ff.positions()[1];
  TEST_ASSERT(RDKit::feq(d.length(), 1.514, 1e-3));

  // minimize in "3D"
  ff.initialize();
  (*ff.positions()[1])[2] = 1.1;
  (*ff.positions()[1])[1] = 0.9;
  (*ff.positions()[1])[0] = 1.00;
  ff.minimize(10, 1e-8);
  d = *(RDGeom::Point3D *)ff.positions()[0] -
      *(RDGeom::Point3D *)ff.positions()[1];
  TEST_ASSERT(RDKit::feq(d.length(), 1.514, 1e-3));

  delete[] p;
  delete[] g;
  std::cerr << "  done" << std::endl;
}

void testUFF3() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for basics of UFF angle terms." << std::endl;

  ForceFields::UFF::AtomicParams p1, p2, p3;
  double restLen, forceConstant;

  // sp3 carbon:
  p3.r1 = .757;
  p3.Z1 = 1.912;
  p3.GMP_Xi = 5.343;
  p3.theta0 = 109.47 * M_PI / 180.0;

  // sp3 - sp3: checks basics
  restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p3, &p3);
  TEST_ASSERT(RDKit::feq(restLen, 1.514));

  // C_3 - C_3 - C_3
  forceConstant = ForceFields::UFF::Utils::calcAngleForceConstant(
      p3.theta0, 1, 1, &p3, &p3, &p3);
  // TEST_ASSERT(RDKit::feq(forceConstant,699.5918));

  // amide bond bend:
  // C_R - N_R - C_3
  // C_R:
  p1.r1 = .729;
  p1.Z1 = 1.912;
  p1.GMP_Xi = 5.343;
  // N_R:
  p2.r1 = .699;
  p2.Z1 = 2.544;
  p2.GMP_Xi = 6.899;
  p2.theta0 = 120.0 * M_PI / 180.;
  restLen = ForceFields::UFF::Utils::calcBondRestLength(
      ForceFields::UFF::Params::amideBondOrder, &p1, &p2);
  TEST_ASSERT(RDKit::feq(restLen, 1.357, 1e-3));
  restLen = ForceFields::UFF::Utils::calcBondRestLength(1.0, &p2, &p3);
  TEST_ASSERT(RDKit::feq(restLen, 1.450, 1e-3));

  forceConstant = ForceFields::UFF::Utils::calcAngleForceConstant(
      p2.theta0, ForceFields::UFF::Params::amideBondOrder, 1, &p1, &p2, &p3);
  TEST_ASSERT(RDKit::feq(forceConstant, 211.0, 1e-1));  //  paper has 105.5

  std::cerr << "  done" << std::endl;
}

void testUFF4() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for UFF angle-bend terms." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1(1.514, 0, 0), p2(0, 0, 0), p3(0.1, 1.5, 0);
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);

  ForceFields::UFF::AtomicParams param1;
  // sp3 carbon:
  param1.r1 = .757;
  param1.Z1 = 1.912;
  param1.GMP_Xi = 5.343;
  // cheat to get the angle to 90 so that testing is easier:
  param1.theta0 = 90.0 * M_PI / 180.;

  // C_3 - C_3, r0=1.514, k01=699.5918
  ForceFields::ForceFieldContrib *contrib;
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 1, &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 2, 1, &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
                                                   &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  RDGeom::Point3D d, v1, v2;
  double theta;
#if 1
  // ------- ------- ------- ------- ------- ------- -------
  // try a bit of minimization
  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[1] -
       *(RDGeom::Point3D *)ff.positions()[2];
  theta = v1.angleTo(v2);

  TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, 90 * M_PI / 180., 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // more complicated atomic coords:
  p1.x = 1.3;
  p1.y = 0.1;
  p1.z = 0.1;
  p2.x = -0.1;
  p2.y = 0.05;
  p2.z = -0.05;
  p3.x = 0.1;
  p3.y = 1.5;
  p3.z = 0.05;
  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[1] -
       *(RDGeom::Point3D *)ff.positions()[2];
  theta = v1.angleTo(v2);

  TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, 90 * M_PI / 180., 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // try for the tetrahedral angle instead of 90:
  param1.theta0 = 109.47 * M_PI / 180.;
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
                                                   &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 1.3;
  p1.y = 0.1;
  p1.z = 0.1;
  p2.x = -0.1;
  p2.y = 0.05;
  p2.z = -0.05;
  p3.x = 0.1;
  p3.y = 1.5;
  p3.z = 0.05;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);
  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[2] -
       *(RDGeom::Point3D *)ff.positions()[1];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));

#endif

  // ------- ------- ------- ------- ------- ------- -------
  //
  // Do a series of "special cases" (i.e. test the functional forms
  // for linear, trigonal planar, square planar and octahedral)
  //
  // ------- ------- ------- ------- ------- ------- -------

  // ------- ------- ------- ------- ------- ------- -------
  // test a linear molecule:
  param1.theta0 = M_PI;
  // ff.contribs().pop_back();
  // ff.contribs().pop_back();
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
                                                   &param1, &param1, 2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 1.3;
  p1.y = 0.1;
  p1.z = 0.0;
  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;
  p3.x = -1.3;
  p3.y = 0.1;
  p3.z = 0.00;
  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[2] -
       *(RDGeom::Point3D *)ff.positions()[1];
  theta = v1.angleTo(v2);

  TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
  std::cerr << "theta = " << theta << "; theta0 = " << param1.theta0
            << std::endl;
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // test n=3:
  param1.theta0 = 120. * M_PI / 180.0;
  // ff.contribs().pop_back();
  // ff.contribs().pop_back();
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
                                                   &param1, &param1, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 1.3;
  p1.y = 0.1;
  p1.z = 0.0;
  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;
  p3.x = -.3;
  p3.y = -1.3;
  p3.z = 0.00;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[2] -
       *(RDGeom::Point3D *)ff.positions()[1];
  theta = v1.angleTo(v2);

  TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
  std::cerr << "theta = " << std::fixed << std::setprecision(6) << theta
            << ", param1.theta0 = " << std::fixed << std::setprecision(6)
            << param1.theta0 << std::endl;
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // test n=4:
  param1.theta0 = M_PI / 2.0;
  // ff.contribs().pop_back();
  // ff.contribs().pop_back();
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 1, 1, &param1,
                                                   &param1, &param1, 4);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 1.3;
  p1.y = 0.1;
  p1.z = 0.0;
  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;
  p3.x = -.3;
  p3.y = -1.3;
  p3.z = 0.00;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[2] -
       *(RDGeom::Point3D *)ff.positions()[1];
  theta = v1.angleTo(v2);

  TEST_ASSERT(RDKit::feq(v1.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), 1.514, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));

#if 0
  std::cerr << " " << *ff.positions()[0] << std::endl;
  std::cerr << " " << *ff.positions()[1] << std::endl;
  std::cerr << " " << *ff.positions()[2] << std::endl;

  std::cerr << "v1: " << v1 << std::endl;
  std::cerr << "v2: " << v2 << std::endl;
  std::cerr << "FINAL: " << v1.angleTo(v2) << " " << v1.signedAngleTo(v2) << std::endl;
#endif

  std::cerr << "  done" << std::endl;
}

void testUFF5() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << " Test Simple UFF molecule optimizations." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1, p2, p3, p4, p5, p6;
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);
  ps.push_back(&p4);
  ps.push_back(&p5);
  ps.push_back(&p6);

  ForceFields::UFF::AtomicParams param1, param2;
  // sp2 carbon:
  param1.r1 = .732;
  param1.Z1 = 1.912;
  param1.GMP_Xi = 5.343;
  param1.theta0 = 120. * M_PI / 180.;

  // H_1:
  param2.r1 = 0.354;
  param2.Z1 = 0.712;
  param2.GMP_Xi = 4.528;

  ForceFields::ForceFieldContrib *contrib;

  // build ethylene:
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 2, &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 2, 1, &param1, &param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 3, 1, &param1, &param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 4, 1, &param1, &param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 5, 1, &param1, &param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 2, 2, 1, &param1,
                                                   &param1, &param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 3, 2, 1, &param1,
                                                   &param1, &param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 2, 0, 3, 1, 1, &param2,
                                                   &param1, &param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 4, 2, 1, &param1,
                                                   &param1, &param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 5, 2, 1, &param1,
                                                   &param1, &param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 4, 1, 5, 1, 1, &param2,
                                                   &param1, &param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  // dodge the fact that we're not using torsions yet by putting
  // everything in the z=0 plane:
  p1.x = -0.58;
  p1.y = -0.33;
  p1.z = 0.0;

  p2.x = 0.58;
  p2.y = 0.33;
  p2.z = 0.0;

  p3.x = -0.61;
  p3.y = -1.43;
  p3.z = 0.0;

  p4.x = -1.54;
  p4.y = 0.20;
  p4.z = 0.0;

  p5.x = 0.61;
  p5.y = 1.43;
  p5.z = 0.0;

  p6.x = 1.54;
  p6.y = -0.20;
  p6.z = 0.0;

  RDGeom::Point3D d, v1, v2;
  double theta;
  // ------- ------- ------- ------- ------- ------- -------
  // try a bit of minimization
  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);

  double CCDblBondLen =
      ForceFields::UFF::Utils::calcBondRestLength(2, &param1, &param1);
  double CHBondLen =
      ForceFields::UFF::Utils::calcBondRestLength(1, &param1, &param2);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[2];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(v1.length(), CCDblBondLen, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));
  v2 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[3];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[2];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(theta, param1.theta0, 1e-4));

  std::cerr << "  done" << std::endl;
}

void testUFF6() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for UFF nonbonded terms." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1(0, 0, 0), p2(0.0, 0, 0);
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);

  ForceFields::UFF::AtomicParams param1;
  // sp3 carbon:
  param1.r1 = .757;
  param1.Z1 = 1.912;
  param1.GMP_Xi = 5.343;
  param1.x1 = 3.851;
  param1.D1 = 0.105;

  ff.initialize();
  ForceFields::ForceFieldContrib *contrib;
  contrib = new ForceFields::UFF::vdWContrib(&ff, 0, 1, &param1, &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  // try a bit of minimization
  RDGeom::Point3D d;
  ff.initialize();

  // edge case: our energy at zero length should be zero:
  double E;
  E = ff.calcEnergy();
  TEST_ASSERT(RDKit::feq(E, 0.0));

  (*ff.positions()[0])[0] = 0.0;
  (*ff.positions()[1])[0] = 4.0;
  ff.minimize(10, 1e-8, 1e-8);
  d = *(RDGeom::Point3D *)ff.positions()[0] -
      *(RDGeom::Point3D *)ff.positions()[1];
  TEST_ASSERT(RDKit::feq(d.length(), 3.851, 1e-3));

  // minimize in "3D"
  ff.initialize();
  (*ff.positions()[0])[0] = 0.0;
  (*ff.positions()[0])[1] = 0.0;
  (*ff.positions()[0])[2] = 0.0;
  (*ff.positions()[1])[2] = 3.1;
  (*ff.positions()[1])[1] = 0.9;
  (*ff.positions()[1])[0] = 1.00;
  ff.minimize(10, 1e-8, 1e-8);
  d = *(RDGeom::Point3D *)ff.positions()[0] -
      *(RDGeom::Point3D *)ff.positions()[1];
  TEST_ASSERT(RDKit::feq(d.length(), 3.851, 1e-3));

  std::cerr << "  done" << std::endl;
}

void testUFF7() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << " Test UFF torsional terms." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1, p2, p3, p4;
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);
  ps.push_back(&p4);

  ForceFields::UFF::AtomicParams param1;
  // sp3 carbon:
  param1.r1 = .757;
  param1.Z1 = 1.912;
  param1.GMP_Xi = 5.343;
  param1.x1 = 3.851;
  param1.D1 = 0.105;
  param1.V1 = 2.119;
  param1.U1 = 2.0;

  RDGeom::Point3D d, v1, v2;
  double cosPhi;

  ForceFields::ForceFieldContrib *contrib;
  // ------- ------- ------- ------- ------- ------- -------
  // Basic SP3 - SP3
  // ------- ------- ------- ------- ------- ------- -------
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, &param1,
      &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
#if 1
  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.0;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);
  cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // Basic SP2 - SP2
  // ------- ------- ------- ------- ------- ------- -------
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP2, &param1,
      &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0.1;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.2;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(10, 1e-8, 1e-8);
  cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 1.0, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // Basic SP2 - SP3
  // ------- ------- ------- ------- ------- ------- -------
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, &param1,
      &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0.1;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.2;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);
  cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // special case for group 6 - group 6 bonds:
  // ------- ------- ------- ------- ------- ------- -------
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 3, 1, 8, 8, RDKit::Atom::SP3, RDKit::Atom::SP3, &param1,
      &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0.1;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.2;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);
  cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 0.0, 1e-4));

  // ------- ------- ------- ------- ------- ------- -------
  // special case for SP3 group 6 - SP2 other group
  // ------- ------- ------- ------- ------- ------- -------
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 3, 1, 8, 6, RDKit::Atom::SP3, RDKit::Atom::SP2, &param1,
      &param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0.1;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.2;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);
  cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 0.0, 1e-4));

#endif

  // ------- ------- ------- ------- ------- ------- -------
  // special case for (SP2 -) SP2 - SP3
  // ------- ------- ------- ------- ------- ------- -------
  ff.contribs().pop_back();
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 3, 1, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, &param1,
      &param1, true);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  p1.x = 0;
  p1.y = 1.5;
  p1.z = 0.1;

  p2.x = 0.0;
  p2.y = 0.0;
  p2.z = 0.0;

  p3.x = 1.5;
  p3.y = 0.0;
  p3.z = 0.0;

  p4.x = 1.5;
  p4.y = 0.2;
  p4.z = 1.5;

  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);
  cosPhi = ForceFields::UFF::Utils::calculateCosTorsion(
      *(RDGeom::Point3D *)ff.positions()[0],
      *(RDGeom::Point3D *)ff.positions()[1],
      *(RDGeom::Point3D *)ff.positions()[2],
      *(RDGeom::Point3D *)ff.positions()[3]);
  TEST_ASSERT(RDKit::feq(cosPhi, 0.5, 1e-4));

  std::cerr << "  done" << std::endl;
}

void testUFFParams() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << " Test UFF Parameter objects" << std::endl;

  ForceFields::UFF::ParamCollection *params =
      ForceFields::UFF::ParamCollection::getParams();
  TEST_ASSERT(params);

  const ForceFields::UFF::AtomicParams *ptr;
  ptr = (*params)("C_3");
  TEST_ASSERT(ptr);
  TEST_ASSERT(RDKit::feq(ptr->r1, 0.757));
  TEST_ASSERT(RDKit::feq(ptr->theta0, 109.47 * M_PI / 180.));
  TEST_ASSERT(RDKit::feq(ptr->x1, 3.851));
  TEST_ASSERT(RDKit::feq(ptr->D1, 0.105));
  TEST_ASSERT(RDKit::feq(ptr->zeta, 12.73));
  TEST_ASSERT(RDKit::feq(ptr->Z1, 1.912));
  TEST_ASSERT(RDKit::feq(ptr->V1, 2.119));
  TEST_ASSERT(RDKit::feq(ptr->GMP_Xi, 5.343));
  TEST_ASSERT(RDKit::feq(ptr->GMP_Hardness, 5.063));
  TEST_ASSERT(RDKit::feq(ptr->GMP_Radius, 0.759));

  ptr = (*params)("N_3");
  TEST_ASSERT(ptr);

  ptr = (*params)("C_5");
  TEST_ASSERT(!ptr);
}

void testUFF8() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << " Test Simple UFF molecule optimization, part 2." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1, p2, p3, p4, p5, p6;
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);
  ps.push_back(&p4);
  ps.push_back(&p5);
  ps.push_back(&p6);

  ForceFields::UFF::ParamCollection *params =
      ForceFields::UFF::ParamCollection::getParams();
  const ForceFields::UFF::AtomicParams *param1, *param2;

  // C_2 (sp2 carbon):
  param1 = (*params)("C_2");
  TEST_ASSERT(param1);
  // H_:
  param2 = (*params)("H_");
  TEST_ASSERT(param2);
  ForceFields::ForceFieldContrib *contrib;

  // build ethylene:
  // BONDS:
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 2, param1, param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 2, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 3, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 4, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 5, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  // ANGLES:
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 2, 2, 1, param1,
                                                   param1, param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 0, 3, 2, 1, param1,
                                                   param1, param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 2, 0, 3, 1, 1, param2,
                                                   param1, param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 4, 2, 1, param1,
                                                   param1, param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 5, 2, 1, param1,
                                                   param1, param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 4, 1, 5, 1, 1, param2,
                                                   param1, param2, 3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  // DIHEDRALS:
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 2, 0, 1, 4, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
      param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 2, 0, 1, 5, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
      param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 3, 0, 1, 4, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
      param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 3, 0, 1, 5, 2, 6, 6, RDKit::Atom::SP3, RDKit::Atom::SP3, param1,
      param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = -0.58;
  p1.y = -0.33;
  p1.z = 0.1;

  p2.x = 0.58;
  p2.y = 0.33;
  p2.z = 0.1;

  p3.x = -0.61;
  p3.y = -1.43;
  p3.z = 0.0;

  p4.x = -1.54;
  p4.y = 0.20;
  p4.z = 0.0;

  p5.x = 0.61;
  p5.y = 1.43;
  p5.z = 0.0;

  p6.x = 1.54;
  p6.y = -0.20;
  p6.z = 0.0;

  RDGeom::Point3D d, v1, v2;
  double theta;
  // ------- ------- ------- ------- ------- ------- -------
  // try a bit of minimization
  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);

  double CCDblBondLen =
      ForceFields::UFF::Utils::calcBondRestLength(2, param1, param1);
  double CHBondLen =
      ForceFields::UFF::Utils::calcBondRestLength(1, param1, param2);

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[1];
  v2 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[2];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(v1.length(), CCDblBondLen, 1e-3));
  TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, param1->theta0, 1e-4));
  v2 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[3];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(v2.length(), CHBondLen, 1e-3));
  TEST_ASSERT(RDKit::feq(theta, param1->theta0, 1e-4));

  v1 = *(RDGeom::Point3D *)ff.positions()[0] -
       *(RDGeom::Point3D *)ff.positions()[2];
  theta = v1.angleTo(v2);
  TEST_ASSERT(RDKit::feq(theta, param1->theta0, 1e-4));

  std::cerr << "  done" << std::endl;
}

void testUFFTorsionConflict() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << " Test UFF Torsion Conflicts." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1, p2, p3, p4, p5, p6, p7;
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);
  ps.push_back(&p3);
  ps.push_back(&p4);
  ps.push_back(&p5);
  ps.push_back(&p6);
  ps.push_back(&p7);

  ForceFields::UFF::ParamCollection *params =
      ForceFields::UFF::ParamCollection::getParams();
  const ForceFields::UFF::AtomicParams *param1, *param2, *param3;

  // C_2 (sp2 carbon):
  param1 = (*params)("C_2");
  TEST_ASSERT(param1);
  // H_:
  param2 = (*params)("H_");
  TEST_ASSERT(param2);
  // C_3 (sp3 carbon):
  param3 = (*params)("C_3");
  TEST_ASSERT(param3);

  ForceFields::ForceFieldContrib *contrib;

  // BONDS:
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 0, 1, 2, param1, param1);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 2, 1, param1, param3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 1, 3, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 2, 4, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 2, 5, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib =
      new ForceFields::UFF::BondStretchContrib(&ff, 2, 6, 1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

#if 1
  // ANGLES:
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 2, 2.0, 1.0,
                                                   param1, param1, param3);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 0, 1, 3, 2.0, 1.0,
                                                   param1, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 2, 4, 1.0, 1.0,
                                                   param1, param3, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 2, 5, 1.0, 1.0,
                                                   param1, param3, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 1, 2, 6, 1.0, 1.0,
                                                   param1, param3, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::AngleBendContrib(&ff, 2, 1, 3, 1.0, 1.0,
                                                   param3, param1, param2);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
#endif

  // DIHEDRALS:
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 4, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
      param3, true);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 3, 1, 2, 4, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
      param3, false);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 5, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
      param3, true);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 3, 1, 2, 5, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
      param3, false);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 0, 1, 2, 6, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
      param3, true);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));
  contrib = new ForceFields::UFF::TorsionAngleContrib(
      &ff, 3, 1, 2, 6, 1.0, 6, 6, RDKit::Atom::SP2, RDKit::Atom::SP3, param1,
      param3, false);
  ff.contribs().push_back(ForceFields::ContribPtr(contrib));

  p1.x = 0.5411;
  p1.y = -0.7741;
  p1.z = 0.0902;

  p2.x = -0.5622;
  p2.y = -0.0368;
  p2.z = 0.1202;

  p3.x = -0.5101;
  p3.y = 1.4485;
  p3.z = 0.0816;

  p4.x = -1.5285;
  p4.y = -0.5341;
  p4.z = 0.1892;

  p5.x = 0.5097;
  p5.y = 1.8065;
  p5.z = 0.1988;

  p6.x = -1.1436;
  p6.y = 1.8781;
  p6.z = 0.8983;

  p7.x = -0.9145;
  p7.y = 1.8185;
  p7.z = -0.8983;

  RDGeom::Point3D d, v1, v2;
  // ------- ------- ------- ------- ------- ------- -------
  // try a bit of minimization
  ff.initialize();
  ff.minimize(100, 1e-8, 1e-8);

#if 1
  std::cerr.setf(std::ios_base::fixed, std::ios_base::floatfield);
  std::cerr.precision(4);
  std::cerr << "C " << *ff.positions()[0] << std::endl;
  std::cerr << "C " << *ff.positions()[1] << std::endl;
  std::cerr << "C " << *ff.positions()[2] << std::endl;
  std::cerr << "H " << *ff.positions()[3] << std::endl;
  std::cerr << "H " << *ff.positions()[4] << std::endl;
  std::cerr << "O " << *ff.positions()[5] << std::endl;
  std::cerr << "F " << *ff.positions()[6] << std::endl;
#endif
  std::cerr << "  done" << std::endl;
}

void testUFFDistanceConstraints() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for UFF distance constraint terms." << std::endl;

  ForceFields::ForceField ff;
  Point3D p1(0, 0, 0), p2(1.514, 0, 0);
  RDGeom::PointPtrVect &ps = ff.positions();
  ps.push_back(&p1);
  ps.push_back(&p2);

  double *p, *g;
  p = new double[6];
  g = new double[6];
  for (int i = 0; i < 6; i++) {
    p[i] = 0.0;
    g[i] = 0.0;
  }
  p[0] = 0;
  p[3] = 1.40;

  ff.initialize();

  // C_3 - C_3, r0=1.514, k01=699.5918
  ForceFields::ForceFieldContrib *bs;
  bs = new ForceFields::UFF::DistanceConstraintContrib(&ff, 0, 1, 1.35, 1.55,
                                                       1000.0);
  ff.contribs().push_back(ForceFields::ContribPtr(bs));
  double E;
  E = bs->getEnergy(p);
  TEST_ASSERT(RDKit::feq(E, 0.0));
  bs->getGrad(p, g);
  for (int i = 0; i < 6; i++) {
    TEST_ASSERT(RDKit::feq(g[i], 0.0));
  }

  ff.initialize();
  (*ff.positions()[1])[0] = 1.20;
  p[3] = 1.20;
  E = bs->getEnergy(p);
  TEST_ASSERT(RDKit::feq(E, 11.25));
  bs->getGrad(p, g);
  TEST_ASSERT(RDKit::feq(g[0], 150.0));
  TEST_ASSERT(RDKit::feq(g[3], -150.0));
  TEST_ASSERT(RDKit::feq(g[1], 0.0));
  TEST_ASSERT(RDKit::feq(g[2], 0.0));
  TEST_ASSERT(RDKit::feq(g[4], 0.0));
  TEST_ASSERT(RDKit::feq(g[5], 0.0));

  // try a bit of minimization
  RDGeom::Point3D d;
  ff.initialize();
  (*ff.positions()[1])[2] = 0.0;
  (*ff.positions()[1])[0] = 1.20;
  ff.minimize(10, 1e-8);
  d = *(RDGeom::Point3D *)ff.positions()[0] -
      *(RDGeom::Point3D *)ff.positions()[1];
  TEST_ASSERT(d.length() >= 1.35)
  TEST_ASSERT(d.length() <= 1.55)

  ff.initialize();
  (*ff.positions()[1])[2] = 0.0;
  (*ff.positions()[1])[0] = 1.70;
  ff.minimize(10, 1e-8);
  d = *(RDGeom::Point3D *)ff.positions()[0] -
      *(RDGeom::Point3D *)ff.positions()[1];
  TEST_ASSERT(d.length() >= 1.35)
  TEST_ASSERT(d.length() <= 1.55)

  delete[] p;
  delete[] g;
  std::cerr << "  done" << std::endl;
}

void testUFFAllConstraints() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for all UFF constraint terms." << std::endl;

  std::string molBlock =
      "butane\n"
      "     RDKit          3D\n"
      "butane\n"
      " 17 16  0  0  0  0  0  0  0  0999 V2000\n"
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.4280    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.7913   -0.2660    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.9040    1.3004   -0.3485 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.5407    2.0271    0.3782 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.5407    1.5664   -1.3411 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.3320    1.3004   -0.3485 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.6953    1.5162   -1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.8080    0.0192    0.0649 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.4447   -0.7431   -0.6243 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.4447   -0.1966    1.0697 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    4.8980    0.0192    0.0649 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.6954    2.0627    0.3408 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.7913   -0.7267   -0.7267 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "   -0.3633    0.7267    0.7267 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "   -0.3633   -0.9926    0.2660 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "   -0.3633    0.2660   -0.9926 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "  1  2  1  0  0  0  0\n"
      "  1 15  1  0  0  0  0\n"
      "  1 16  1  0  0  0  0\n"
      "  1 17  1  0  0  0  0\n"
      "  2  3  1  0  0  0  0\n"
      "  2  4  1  0  0  0  0\n"
      "  2 14  1  0  0  0  0\n"
      "  4  5  1  0  0  0  0\n"
      "  4  6  1  0  0  0  0\n"
      "  4  7  1  0  0  0  0\n"
      "  7  8  1  0  0  0  0\n"
      "  7  9  1  0  0  0  0\n"
      "  7 13  1  0  0  0  0\n"
      "  9 10  1  0  0  0  0\n"
      "  9 11  1  0  0  0  0\n"
      "  9 12  1  0  0  0  0\n"
      "M  END\n";
  RDKit::RWMol *mol;
  ForceFields::ForceField *field;

  // distance constraints
  ForceFields::UFF::DistanceConstraintContrib *dc;
  mol = RDKit::MolBlockToMol(molBlock, true, false);
  TEST_ASSERT(mol);
  MolTransforms::setBondLength(mol->getConformer(), 1, 3, 2.0);
  field = RDKit::UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  dc = new ForceFields::UFF::DistanceConstraintContrib(field, 1, 3, 2.0, 2.0,
                                                       1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(dc));
  field->minimize();
  TEST_ASSERT(RDKit::feq(
      MolTransforms::getBondLength(mol->getConformer(), 1, 3), 2.0, 0.1));
  delete field;
  field = RDKit::UFF::constructForceField(*mol);
  field->initialize();
  dc = new ForceFields::UFF::DistanceConstraintContrib(field, 1, 3, true, -0.2,
                                                       0.2, 1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(dc));
  field->minimize();
  TEST_ASSERT(MolTransforms::getBondLength(mol->getConformer(), 1, 3) > 1.79);
  delete field;
  delete mol;

  // angle constraints
  ForceFields::UFF::AngleConstraintContrib *ac;
  mol = RDKit::MolBlockToMol(molBlock, true, false);
  TEST_ASSERT(mol);
  MolTransforms::setAngleDeg(mol->getConformer(), 1, 3, 6, 90.0);
  field = RDKit::UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  ac = new ForceFields::UFF::AngleConstraintContrib(field, 1, 3, 6, 90.0, 90.0,
                                                    1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(ac));
  field->minimize();
  TEST_ASSERT(RDKit::feq(
      MolTransforms::getAngleDeg(mol->getConformer(), 1, 3, 6), 90.0, 0.5));
  delete field;
  field = RDKit::UFF::constructForceField(*mol);
  field->initialize();
  ac = new ForceFields::UFF::AngleConstraintContrib(field, 1, 3, 6, true, -10.0,
                                                    10.0, 1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(ac));
  field->minimize();
  TEST_ASSERT(RDKit::feq(
      MolTransforms::getAngleDeg(mol->getConformer(), 1, 3, 6), 100.0, 0.5));
  delete field;
  MolTransforms::setAngleDeg(mol->getConformer(), 1, 3, 6, 0.0);
  field = RDKit::UFF::constructForceField(*mol);
  field->initialize();
  ac = new ForceFields::UFF::AngleConstraintContrib(field, 1, 3, 6, false,
                                                    -10.0, 10.0, 1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(ac));
  field->minimize();
  TEST_ASSERT(RDKit::feq(
      MolTransforms::getAngleDeg(mol->getConformer(), 1, 3, 6), 10.0, 0.5));
  delete field;
  delete mol;

  // torsion constraints
  ForceFields::UFF::TorsionConstraintContrib *tc;
  mol = RDKit::MolBlockToMol(molBlock, true, false);
  TEST_ASSERT(mol);
  MolTransforms::setDihedralDeg(mol->getConformer(), 1, 3, 6, 8, 15.0);
  field = RDKit::UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  tc = new ForceFields::UFF::TorsionConstraintContrib(field, 1, 3, 6, 8, 10.0,
                                                      20.0, 1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(tc));
  field->minimize();
  TEST_ASSERT(
      RDKit::feq(MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8),
                 20.0, 0.5));
  delete field;
  MolTransforms::setDihedralDeg(mol->getConformer(), 1, 3, 6, 8, -30.0);
  field = RDKit::UFF::constructForceField(*mol);
  field->initialize();
  tc = new ForceFields::UFF::TorsionConstraintContrib(field, 1, 3, 6, 8, true,
                                                      -10.0, 8.0, 1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(tc));
  field->minimize();
  TEST_ASSERT(
      RDKit::feq(MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8),
                 -40.0, 0.5));
  delete field;
  MolTransforms::setDihedralDeg(mol->getConformer(), 1, 3, 6, 8, -10.0);
  field = RDKit::UFF::constructForceField(*mol);
  field->initialize();
  tc = new ForceFields::UFF::TorsionConstraintContrib(field, 1, 3, 6, 8, false,
                                                      -10.0, 8.0, 1.0e6);
  field->contribs().push_back(ForceFields::ContribPtr(tc));
  field->minimize(500);
  TEST_ASSERT(
      RDKit::feq(MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8),
                 -10.0, 0.5));
  delete field;
  delete mol;

  // position constraints
  ForceFields::UFF::PositionConstraintContrib *pc;
  mol = RDKit::MolBlockToMol(molBlock, true, false);
  TEST_ASSERT(mol);
  field = RDKit::UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  RDGeom::Point3D p = mol->getConformer().getAtomPos(1);
  pc = new ForceFields::UFF::PositionConstraintContrib(field, 1, 0.3, 1.0e5);
  field->contribs().push_back(ForceFields::ContribPtr(pc));
  field->minimize();
  RDGeom::Point3D q = mol->getConformer().getAtomPos(1);
  TEST_ASSERT((p - q).length() < 0.3);
  delete field;
  delete mol;

  // fixed atoms
  mol = RDKit::MolBlockToMol(molBlock, true, false);
  TEST_ASSERT(mol);
  field = RDKit::UFF::constructForceField(*mol);
  TEST_ASSERT(field);
  field->initialize();
  RDGeom::Point3D fp = mol->getConformer().getAtomPos(1);
  field->fixedPoints().push_back(1);
  field->minimize();
  RDGeom::Point3D fq = mol->getConformer().getAtomPos(1);
  TEST_ASSERT((fp - fq).length() < 0.01);
  delete field;
  delete mol;

  std::cerr << "  done" << std::endl;
}

void testUFFCopy() {
  std::cerr << "-------------------------------------" << std::endl;
  std::cerr << "Unit tests for copying UFF ForceFields." << std::endl;

  std::string molBlock =
      "butane\n"
      "     RDKit          3D\n"
      "butane\n"
      " 17 16  0  0  0  0  0  0  0  0999 V2000\n"
      "    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.4280    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.7913   -0.2660    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.9040    1.3004   -0.3485 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.5407    2.0271    0.3782 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.5407    1.5664   -1.3411 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.3320    1.3004   -0.3485 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.6953    1.5162   -1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.8080    0.0192    0.0649 C   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.4447   -0.7431   -0.6243 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.4447   -0.1966    1.0697 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    4.8980    0.0192    0.0649 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    3.6954    2.0627    0.3408 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "    1.7913   -0.7267   -0.7267 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "   -0.3633    0.7267    0.7267 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "   -0.3633   -0.9926    0.2660 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "   -0.3633    0.2660   -0.9926 H   0  0  0  0  0  0  0  0  0  0  0  0\n"
      "  1  2  1  0  0  0  0\n"
      "  1 15  1  0  0  0  0\n"
      "  1 16  1  0  0  0  0\n"
      "  1 17  1  0  0  0  0\n"
      "  2  3  1  0  0  0  0\n"
      "  2  4  1  0  0  0  0\n"
      "  2 14  1  0  0  0  0\n"
      "  4  5  1  0  0  0  0\n"
      "  4  6  1  0  0  0  0\n"
      "  4  7  1  0  0  0  0\n"
      "  7  8  1  0  0  0  0\n"
      "  7  9  1  0  0  0  0\n"
      "  7 13  1  0  0  0  0\n"
      "  9 10  1  0  0  0  0\n"
      "  9 11  1  0  0  0  0\n"
      "  9 12  1  0  0  0  0\n"
      "M  END\n";
  {
    RDKit::RWMol *mol = RDKit::MolBlockToMol(molBlock, true, false);
    TEST_ASSERT(mol);
    auto *cmol = new RDKit::RWMol(*mol);
    TEST_ASSERT(cmol);

    ForceFields::ForceField *field = RDKit::UFF::constructForceField(*mol);
    TEST_ASSERT(field);
    field->initialize();
    auto *dc = new ForceFields::UFF::DistanceConstraintContrib(field, 1, 3, 2.0,
                                                               2.0, 1.0e5);
    field->contribs().push_back(ForceFields::ContribPtr(dc));
    field->minimize();
    TEST_ASSERT(MolTransforms::getBondLength(mol->getConformer(), 1, 3) > 1.99);

    auto *cfield = new ForceFields::ForceField(*field);
    cfield->positions().clear();

    for (unsigned int i = 0; i < cmol->getNumAtoms(); i++) {
      cfield->positions().push_back(&cmol->getConformer().getAtomPos(i));
    }
    cfield->initialize();
    cfield->minimize();
    TEST_ASSERT(MolTransforms::getBondLength(cmol->getConformer(), 1, 3) >
                1.99);
    TEST_ASSERT(RDKit::feq(field->calcEnergy(), cfield->calcEnergy()));

    const RDKit::Conformer &conf = mol->getConformer();
    const RDKit::Conformer &cconf = cmol->getConformer();
    for (unsigned int i = 0; i < mol->getNumAtoms(); i++) {
      RDGeom::Point3D p = conf.getAtomPos(i);
      RDGeom::Point3D cp = cconf.getAtomPos(i);
      TEST_ASSERT(RDKit::feq(p.x, cp.x));
      TEST_ASSERT(RDKit::feq(p.y, cp.y));
      TEST_ASSERT(RDKit::feq(p.z, cp.z));
    }

    delete field;
    delete cfield;
    delete mol;
    delete cmol;
  }
  std::cerr << "  done" << std::endl;
}

int main() {
#if 1
  test1();
  testUFF1();
  testUFF2();
  testUFF3();
  testUFF4();
  testUFF5();
  testUFF6();
  testUFF7();
  testUFFParams();
  testUFF8();
  testUFFTorsionConflict();

#endif
  testUFFDistanceConstraints();
  testUFFAllConstraints();
  testUFFCopy();
}