import copy
import math
import os
import pickle
import sys
import unittest

from rdkit import DataStructs, RDConfig
from rdkit.Geometry import rdGeometry as geom


def feq(v1, v2, tol=1.0e-4):
  return abs(v1 - v2) < tol


class TestCase(unittest.TestCase):

  def setUp(self):
    pass

  def test1aPoint3D(self):
    pt = geom.Point3D()
    self.assertTrue(feq(pt.x, 0.0))
    self.assertTrue(feq(pt.y, 0.0))
    self.assertTrue(feq(pt.z, 0.0))

    pt = geom.Point3D(3., 4., 5.)
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt.z, 5.0))
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[1], 4.0))
    self.assertTrue(feq(pt[2], 5.0))
    self.assertTrue(feq(pt[-3], 3.0))
    self.assertTrue(feq(pt[-2], 4.0))
    self.assertTrue(feq(pt[-1], 5.0))
    lst = list(pt)
    self.assertTrue(feq(lst[0], 3.0))
    self.assertTrue(feq(lst[1], 4.0))
    self.assertTrue(feq(lst[2], 5.0))

    pt2 = geom.Point3D(1., 1., 1.)

    pt3 = pt + pt2
    self.assertTrue(feq(pt3.x, 4.0))
    self.assertTrue(feq(pt3.y, 5.0))
    self.assertTrue(feq(pt3.z, 6.0))

    pt += pt2
    self.assertTrue(feq(pt.x, 4.0))
    self.assertTrue(feq(pt.y, 5.0))
    self.assertTrue(feq(pt.z, 6.0))

    pt3 = pt - pt2
    self.assertTrue(feq(pt3.x, 3.0))
    self.assertTrue(feq(pt3.y, 4.0))
    self.assertTrue(feq(pt3.z, 5.0))

    pt -= pt2
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt.z, 5.0))

    pt *= 2.0
    self.assertTrue(feq(pt.x, 6.0))
    self.assertTrue(feq(pt.y, 8.0))
    self.assertTrue(feq(pt.z, 10.0))

    pt /= 2
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt.z, 5.0))
    self.assertTrue(feq(pt.Length(), 7.0711))
    self.assertTrue(feq(pt.LengthSq(), 50.0))
    pt.Normalize()
    self.assertTrue(feq(pt.Length(), 1.0))

    pt1 = geom.Point3D(1.0, 0.0, 0.0)
    pt2 = geom.Point3D(2.0 * math.cos(math.pi / 6), 2.0 * math.sin(math.pi / 6), 0.0)
    ang = pt1.AngleTo(pt2)
    self.assertTrue(feq(ang, math.pi / 6))

    prod = pt1.DotProduct(pt2)
    self.assertTrue(feq(prod, 2.0 * math.cos(math.pi / 6)))

    pt3 = pt1.CrossProduct(pt2)
    self.assertTrue(feq(pt3.x, 0.0))
    self.assertTrue(feq(pt3.y, 0.0))
    self.assertTrue(feq(pt3.z, 1.0))

  def test1bPoint2D(self):
    pt = geom.Point2D()
    self.assertTrue(feq(pt.x, 0.0))
    self.assertTrue(feq(pt.y, 0.0))

    pt = geom.Point2D(3., 4.)
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))

    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[1], 4.0))
    self.assertTrue(feq(pt[-2], 3.0))
    self.assertTrue(feq(pt[-1], 4.0))
    lst = list(pt)
    self.assertTrue(feq(lst[0], 3.0))
    self.assertTrue(feq(lst[1], 4.0))

    pt2 = geom.Point2D(1., 1.)

    pt3 = pt + pt2
    self.assertTrue(feq(pt3.x, 4.0))
    self.assertTrue(feq(pt3.y, 5.0))

    pt += pt2
    self.assertTrue(feq(pt.x, 4.0))
    self.assertTrue(feq(pt.y, 5.0))

    pt3 = pt - pt2
    self.assertTrue(feq(pt3.x, 3.0))
    self.assertTrue(feq(pt3.y, 4.0))

    pt -= pt2
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))

    pt *= 2.0
    self.assertTrue(feq(pt.x, 6.0))
    self.assertTrue(feq(pt.y, 8.0))

    pt /= 2
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt.Length(), 5.0))
    self.assertTrue(feq(pt.LengthSq(), 25.0))
    pt.Normalize()
    self.assertTrue(feq(pt.Length(), 1.0))

    pt1 = geom.Point2D(1.0, 0.0)
    pt2 = geom.Point2D(2.0 * math.cos(math.pi / 6), 2.0 * math.sin(math.pi / 6))
    ang = pt1.AngleTo(pt2)
    self.assertTrue(feq(ang, math.pi / 6))

    prod = pt1.DotProduct(pt2)
    self.assertTrue(feq(prod, 2.0 * math.cos(math.pi / 6)))

  def test1cPointND(self):
    dim = 4
    pt = geom.PointND(4)
    for i in range(dim):
      self.assertTrue(feq(pt[i], 0.0))

    pt[0] = 3
    pt[3] = 4
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[3], 4.0))
    self.assertTrue(feq(pt[-4], 3.0))
    self.assertTrue(feq(pt[-1], 4.0))
    lst = list(pt)
    self.assertTrue(feq(lst[0], 3.0))
    self.assertTrue(feq(lst[3], 4.0))

    pt2 = geom.PointND(4)
    pt2[0] = 1.
    pt2[2] = 1.

    pt3 = pt + pt2
    self.assertTrue(feq(pt3[0], 4.0))
    self.assertTrue(feq(pt3[2], 1.0))
    self.assertTrue(feq(pt3[3], 4.0))

    pt += pt2
    self.assertTrue(feq(pt[0], 4.0))
    self.assertTrue(feq(pt[2], 1.0))
    self.assertTrue(feq(pt[3], 4.0))

    pt3 = pt - pt2
    self.assertTrue(feq(pt3[0], 3.0))
    self.assertTrue(feq(pt3[2], 0.0))
    self.assertTrue(feq(pt3[3], 4.0))

    pt -= pt2
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[2], 0.0))
    self.assertTrue(feq(pt[3], 4.0))

    pt *= 2.0
    self.assertTrue(feq(pt[0], 6.0))
    self.assertTrue(feq(pt[1], 0.0))
    self.assertTrue(feq(pt[2], 0.0))
    self.assertTrue(feq(pt[3], 8.0))

    pt /= 2
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[1], 0.0))
    self.assertTrue(feq(pt[2], 0.0))
    self.assertTrue(feq(pt[3], 4.0))

    self.assertTrue(feq(pt.Length(), 5.0))
    self.assertTrue(feq(pt.LengthSq(), 25.0))
    pt.Normalize()
    self.assertTrue(feq(pt.Length(), 1.0))

    pkl = pickle.dumps(pt)
    pt2 = pickle.loads(pkl)
    self.assertTrue(len(pt) == len(pt2))
    for i in range(len(pt)):
      self.assertTrue(feq(pt2[i], pt[i]))

  def test3UniformGrid(self):
    ugrid = geom.UniformGrid3D(20, 18, 15)
    self.assertTrue(ugrid.GetNumX() == 40)
    self.assertTrue(ugrid.GetNumY() == 36)
    self.assertTrue(ugrid.GetNumZ() == 30)
    dvect = ugrid.GetOccupancyVect()
    ugrid = geom.UniformGrid3D(20, 18, 15, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE)
    dvect = ugrid.GetOccupancyVect()
    self.assertTrue(dvect.GetValueType() == DataStructs.DiscreteValueType.TWOBITVALUE)

    grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)

    geom.WriteGridToFile(grd, "junk.grd")
    grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)

    dist = geom.TanimotoDistance(grd, grd2)
    self.assertTrue(dist == 0.25)
    dist = geom.ProtrudeDistance(grd, grd2)
    self.assertTrue(dist == 0.25)
    dist = geom.ProtrudeDistance(grd2, grd)
    self.assertTrue(dist == 0.0)

    grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5, DataStructs.DiscreteValueType.FOURBITVALUE)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25, 3)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25, 3)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25, 3)
    self.assertRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))

    grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 1.0)
    self.assertRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))

    grd2 = geom.UniformGrid3D(11.0, 10.0, 10.0, 1.0)
    self.assertRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))

  def testSymmetry(self):
    grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
    grd.SetSphereOccupancy(geom.Point3D(-2.2, -2.0, 0.0), 1.65, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.2, -2.0, 0.0), 1.65, 0.25)

    bPt1 = geom.Point3D(-4.0, -2.0, -2.0)
    bPt2 = geom.Point3D(4.0, -2.0, -2.0)
    for k in range(8):
      bPt1 += geom.Point3D(0.0, 0.0, 0.5)
      bPt2 += geom.Point3D(0.0, 0.0, 0.5)
      for j in range(8):
        bPt1 += geom.Point3D(0.0, 0.5, 0.0)
        bPt2 += geom.Point3D(0.0, 0.5, 0.0)
        for i in range(8):
          bPt1 += geom.Point3D(0.5, 0.0, 0.0)
          bPt2 -= geom.Point3D(0.5, 0.0, 0.0)
          self.assertTrue(grd.GetValPoint(bPt1) == grd.GetValPoint(bPt2))

        bPt1.x = -4.0
        bPt2.x = 4.0
      bPt1.y = -2.0
      bPt2.y = -2.0

  def testPointPickles(self):
    pt = geom.Point3D(2.0, -3.0, 1.0)
    pt2 = pickle.loads(pickle.dumps(pt))
    self.assertTrue(feq(pt.x, pt2.x, 1e-6))
    self.assertTrue(feq(pt.y, pt2.y, 1e-6))
    self.assertTrue(feq(pt.z, pt2.z, 1e-6))

    pt = geom.Point2D(2.0, -4.0)
    pt2 = pickle.loads(pickle.dumps(pt))
    self.assertTrue(feq(pt.x, pt2.x, 1e-6))
    self.assertTrue(feq(pt.y, pt2.y, 1e-6))

  def test4GridPickles(self):
    grd = geom.UniformGrid3D(10.0, 9.0, 8.0, 0.5)
    self.assertTrue(grd.GetNumX() == 20)
    self.assertTrue(grd.GetNumY() == 18)
    self.assertTrue(grd.GetNumZ() == 16)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)

    self.assertTrue(geom.TanimotoDistance(grd, grd) == 0.0)

    grd2 = pickle.loads(pickle.dumps(grd))
    self.assertTrue(grd2.GetNumX() == 20)
    self.assertTrue(grd2.GetNumY() == 18)
    self.assertTrue(grd2.GetNumZ() == 16)
    self.assertTrue(geom.TanimotoDistance(grd, grd2) == 0.0)

  def test5GridOps(self):
    grd = geom.UniformGrid3D(10, 10, 10)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.0, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.0, 0.25)

    grd2 = geom.UniformGrid3D(10, 10, 10)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.0, 0.25)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.0, 0.25)

    self.assertTrue(geom.TanimotoDistance(grd, grd) == 0.0)
    self.assertTrue(geom.TanimotoDistance(grd, grd2) == 1.0)

    grd3 = copy.deepcopy(grd)
    grd3 |= grd2
    self.assertTrue(geom.TanimotoDistance(grd3, grd) == .5)
    self.assertTrue(geom.TanimotoDistance(grd3, grd2) == .5)

    grd3 = copy.deepcopy(grd)
    grd3 += grd2
    self.assertTrue(geom.TanimotoDistance(grd3, grd) == .5)
    self.assertTrue(geom.TanimotoDistance(grd3, grd2) == .5)

    grd3 -= grd
    self.assertTrue(geom.TanimotoDistance(grd3, grd) == 1.0)
    self.assertTrue(geom.TanimotoDistance(grd3, grd2) == 0)

    grd4 = geom.UniformGrid3D(10, 10, 10)
    grd4.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.0, 0.25)
    grd4.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.0, 0.25)
    grd4.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.0, 0.25)
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd), .3333))
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd2), .75))

    grd4 &= grd2
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd), 1.0))
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd2), .5))

  def test6Dihedrals(self):
    p1 = geom.Point3D(1, 0, 0)
    p2 = geom.Point3D(0, 0, 0)
    p3 = geom.Point3D(0, 1, 0)

    p4 = geom.Point3D(.5, 1, .5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, -math.pi / 4, 4)

    p4 = geom.Point3D(-.5, 1, .5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 3 * math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, -3 * math.pi / 4, 4)

    p4 = geom.Point3D(.5, 1, -.5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 4, 4)

    p4 = geom.Point3D(-.5, 1, -.5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 3 * math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 3 * math.pi / 4, 4)

    p4 = geom.Point3D(0, 1, 1)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 2, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, -math.pi / 2, 4)

    p4 = geom.Point3D(0, 1, -1)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 2, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 2, 4)

    p4 = geom.Point3D(1, 1, 0)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 0, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 0, 4)

    p4 = geom.Point3D(-1, 1, 0)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi, 4)

  def test7UniformGridIndices(self):
    ugrid = geom.UniformGrid3D(20, 18, 15)
    idx = ugrid.GetGridIndex(3, 2, 1)
    xi, yi, zi = ugrid.GetGridIndices(idx)
    self.assertEqual(xi, 3)
    self.assertEqual(yi, 2)
    self.assertEqual(zi, 1)

  def test8InitPoint2DFromPoint3D(self):
    p3 = geom.Point3D(1., 2., 3.)
    p2 = geom.Point2D(p3)
    self.assertEqual(p2.x, p3.x)
    self.assertEqual(p2.y, p3.y)

  def test1bPoint2D(self):
    pt = geom.Point2D()
    self.assertTrue(feq(pt.x, 0.0))
    self.assertTrue(feq(pt.y, 0.0))

    pt = geom.Point2D(3., 4.)
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))

    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[1], 4.0))
    self.assertTrue(feq(pt[-2], 3.0))
    self.assertTrue(feq(pt[-1], 4.0))
    lst = list(pt)
    self.assertTrue(feq(lst[0], 3.0))
    self.assertTrue(feq(lst[1], 4.0))

    pt2 = geom.Point2D(1., 1.)

    pt3 = pt + pt2
    self.assertTrue(feq(pt3.x, 4.0))
    self.assertTrue(feq(pt3.y, 5.0))

    pt += pt2
    self.assertTrue(feq(pt.x, 4.0))
    self.assertTrue(feq(pt.y, 5.0))

    pt3 = pt - pt2
    self.assertTrue(feq(pt3.x, 3.0))
    self.assertTrue(feq(pt3.y, 4.0))

    pt -= pt2
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))

    pt *= 2.0
    self.assertTrue(feq(pt.x, 6.0))
    self.assertTrue(feq(pt.y, 8.0))

    pt /= 2
    self.assertTrue(feq(pt.x, 3.0))
    self.assertTrue(feq(pt.y, 4.0))
    self.assertTrue(feq(pt.Length(), 5.0))
    self.assertTrue(feq(pt.LengthSq(), 25.0))
    pt.Normalize()
    self.assertTrue(feq(pt.Length(), 1.0))

    pt1 = geom.Point2D(1.0, 0.0)
    pt2 = geom.Point2D(2.0 * math.cos(math.pi / 6), 2.0 * math.sin(math.pi / 6))
    ang = pt1.AngleTo(pt2)
    self.assertTrue(feq(ang, math.pi / 6))

    prod = pt1.DotProduct(pt2)
    self.assertTrue(feq(prod, 2.0 * math.cos(math.pi / 6)))

  def test1cPointND(self):
    dim = 4
    pt = geom.PointND(4)
    for i in range(dim):
      self.assertTrue(feq(pt[i], 0.0))

    pt[0] = 3
    pt[3] = 4
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[3], 4.0))
    self.assertTrue(feq(pt[-4], 3.0))
    self.assertTrue(feq(pt[-1], 4.0))
    lst = list(pt)
    self.assertTrue(feq(lst[0], 3.0))
    self.assertTrue(feq(lst[3], 4.0))

    pt2 = geom.PointND(4)
    pt2[0] = 1.
    pt2[2] = 1.

    pt3 = pt + pt2
    self.assertTrue(feq(pt3[0], 4.0))
    self.assertTrue(feq(pt3[2], 1.0))
    self.assertTrue(feq(pt3[3], 4.0))

    pt += pt2
    self.assertTrue(feq(pt[0], 4.0))
    self.assertTrue(feq(pt[2], 1.0))
    self.assertTrue(feq(pt[3], 4.0))

    pt3 = pt - pt2
    self.assertTrue(feq(pt3[0], 3.0))
    self.assertTrue(feq(pt3[2], 0.0))
    self.assertTrue(feq(pt3[3], 4.0))

    pt -= pt2
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[2], 0.0))
    self.assertTrue(feq(pt[3], 4.0))

    pt *= 2.0
    self.assertTrue(feq(pt[0], 6.0))
    self.assertTrue(feq(pt[1], 0.0))
    self.assertTrue(feq(pt[2], 0.0))
    self.assertTrue(feq(pt[3], 8.0))

    pt /= 2
    self.assertTrue(feq(pt[0], 3.0))
    self.assertTrue(feq(pt[1], 0.0))
    self.assertTrue(feq(pt[2], 0.0))
    self.assertTrue(feq(pt[3], 4.0))

    self.assertTrue(feq(pt.Length(), 5.0))
    self.assertTrue(feq(pt.LengthSq(), 25.0))
    pt.Normalize()
    self.assertTrue(feq(pt.Length(), 1.0))

    pkl = pickle.dumps(pt)
    pt2 = pickle.loads(pkl)
    self.assertTrue(len(pt) == len(pt2))
    for i in range(len(pt)):
      self.assertTrue(feq(pt2[i], pt[i]))

  def test3UniformGrid(self):
    ugrid = geom.UniformGrid3D(20, 18, 15)
    self.assertTrue(ugrid.GetNumX() == 40)
    self.assertTrue(ugrid.GetNumY() == 36)
    self.assertTrue(ugrid.GetNumZ() == 30)
    dvect = ugrid.GetOccupancyVect()
    ugrid = geom.UniformGrid3D(20, 18, 15, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE)
    dvect = ugrid.GetOccupancyVect()
    self.assertTrue(dvect.GetValueType() == DataStructs.DiscreteValueType.TWOBITVALUE)

    grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)

    geom.WriteGridToFile(grd, "junk.grd")
    grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)

    dist = geom.TanimotoDistance(grd, grd2)
    self.assertTrue(dist == 0.25)
    dist = geom.ProtrudeDistance(grd, grd2)
    self.assertTrue(dist == 0.25)
    dist = geom.ProtrudeDistance(grd2, grd)
    self.assertTrue(dist == 0.0)

    grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5, DataStructs.DiscreteValueType.FOURBITVALUE)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25, 3)
    grd2.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25, 3)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25, 3)
    self.assertRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))

    grd2 = geom.UniformGrid3D(10.0, 10.0, 10.0, 1.0)
    self.assertRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))

    grd2 = geom.UniformGrid3D(11.0, 10.0, 10.0, 1.0)
    self.assertRaises(ValueError, lambda: geom.TanimotoDistance(grd, grd2))

  def testSymmetry(self):
    grd = geom.UniformGrid3D(10.0, 10.0, 10.0, 0.5)
    grd.SetSphereOccupancy(geom.Point3D(-2.2, -2.0, 0.0), 1.65, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.2, -2.0, 0.0), 1.65, 0.25)

    bPt1 = geom.Point3D(-4.0, -2.0, -2.0)
    bPt2 = geom.Point3D(4.0, -2.0, -2.0)
    for k in range(8):
      bPt1 += geom.Point3D(0.0, 0.0, 0.5)
      bPt2 += geom.Point3D(0.0, 0.0, 0.5)
      for j in range(8):
        bPt1 += geom.Point3D(0.0, 0.5, 0.0)
        bPt2 += geom.Point3D(0.0, 0.5, 0.0)
        for i in range(8):
          bPt1 += geom.Point3D(0.5, 0.0, 0.0)
          bPt2 -= geom.Point3D(0.5, 0.0, 0.0)
          self.assertTrue(grd.GetValPoint(bPt1) == grd.GetValPoint(bPt2))

        bPt1.x = -4.0
        bPt2.x = 4.0
      bPt1.y = -2.0
      bPt2.y = -2.0

  def test4UniformRealValueGrid(self):
    ugrid = geom.UniformRealValueGrid3D(20, 18, 15)
    self.assertTrue(ugrid.GetNumX() == 40)
    self.assertTrue(ugrid.GetNumY() == 36)
    self.assertTrue(ugrid.GetNumZ() == 30)
    dvect = ugrid.GetOccupancyVect()
    ugrid = geom.UniformRealValueGrid3D(20, 18, 15, 0.5)
    ugrid.SetVal(50, 2.3)
    val = ugrid.GetVal(50)
    self.assertTrue(feq(val, 2.3))

  def test5PointPickles(self):
    pt = geom.Point3D(2.0, -3.0, 1.0)
    pt2 = pickle.loads(pickle.dumps(pt))
    self.assertTrue(feq(pt.x, pt2.x, 1e-6))
    self.assertTrue(feq(pt.y, pt2.y, 1e-6))
    self.assertTrue(feq(pt.z, pt2.z, 1e-6))

    pt = geom.Point2D(2.0, -4.0)
    pt2 = pickle.loads(pickle.dumps(pt))
    self.assertTrue(feq(pt.x, pt2.x, 1e-6))
    self.assertTrue(feq(pt.y, pt2.y, 1e-6))

  def test6GridPickles(self):
    grd = geom.UniformGrid3D(10.0, 9.0, 8.0, 0.5)
    self.assertTrue(grd.GetNumX() == 20)
    self.assertTrue(grd.GetNumY() == 18)
    self.assertTrue(grd.GetNumZ() == 16)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.5, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.5, 0.25)

    self.assertTrue(geom.TanimotoDistance(grd, grd) == 0.0)

    grd2 = pickle.loads(pickle.dumps(grd))
    self.assertTrue(grd2.GetNumX() == 20)
    self.assertTrue(grd2.GetNumY() == 18)
    self.assertTrue(grd2.GetNumZ() == 16)
    self.assertTrue(geom.TanimotoDistance(grd, grd2) == 0.0)

  def test7RealGridPickles(self):
    grd = geom.UniformRealValueGrid3D(10.0, 9.0, 8.0, 0.5)
    self.assertTrue(grd.GetNumX() == 20)
    self.assertTrue(grd.GetNumY() == 18)
    self.assertTrue(grd.GetNumZ() == 16)

    grd2 = pickle.loads(pickle.dumps(grd))
    self.assertTrue(grd2.GetNumX() == 20)
    self.assertTrue(grd2.GetNumY() == 18)
    self.assertTrue(grd2.GetNumZ() == 16)

  def test8GridOps(self):
    grd = geom.UniformGrid3D(10, 10, 10)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.0, 0.25)
    grd.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.0, 0.25)

    grd2 = geom.UniformGrid3D(10, 10, 10)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.0, 0.25)
    grd2.SetSphereOccupancy(geom.Point3D(2.0, 2.0, 0.0), 1.0, 0.25)

    self.assertTrue(geom.TanimotoDistance(grd, grd) == 0.0)
    self.assertTrue(geom.TanimotoDistance(grd, grd2) == 1.0)

    grd3 = copy.deepcopy(grd)
    grd3 |= grd2
    self.assertTrue(geom.TanimotoDistance(grd3, grd) == .5)
    self.assertTrue(geom.TanimotoDistance(grd3, grd2) == .5)

    grd3 = copy.deepcopy(grd)
    grd3 += grd2
    self.assertTrue(geom.TanimotoDistance(grd3, grd) == .5)
    self.assertTrue(geom.TanimotoDistance(grd3, grd2) == .5)

    grd3 -= grd
    self.assertTrue(geom.TanimotoDistance(grd3, grd) == 1.0)
    self.assertTrue(geom.TanimotoDistance(grd3, grd2) == 0)

    grd4 = geom.UniformGrid3D(10, 10, 10)
    grd4.SetSphereOccupancy(geom.Point3D(-2.0, -2.0, 0.0), 1.0, 0.25)
    grd4.SetSphereOccupancy(geom.Point3D(-2.0, 2.0, 0.0), 1.0, 0.25)
    grd4.SetSphereOccupancy(geom.Point3D(2.0, -2.0, 0.0), 1.0, 0.25)
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd), .3333))
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd2), .75))

    grd4 &= grd2
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd), 1.0))
    self.assertTrue(feq(geom.TanimotoDistance(grd4, grd2), .5))

  def test9RealGridOps(self):
    grd1 = geom.UniformRealValueGrid3D(5.0, 5.0, 5.0, 0.1)
    grd2 = geom.UniformRealValueGrid3D(5.0, 5.0, 5.0, 0.1)

    grd1.SetVal(50, 37.37)
    grd2.SetVal(50, 1.03)
    grd3 = copy.deepcopy(grd2)
    grd4 = geom.UniformRealValueGrid3D(grd2)

    grd1 |= grd2
    self.assertTrue(feq(grd1.GetVal(50), 37.37))
    self.assertTrue(feq(grd2.GetVal(50), 1.03))

    grd2 |= grd1
    self.assertTrue(feq(grd1.GetVal(50), 37.37))
    self.assertTrue(feq(grd2.GetVal(50), 37.37))

    grd2 &= grd3
    self.assertTrue(feq(grd2.GetVal(50), 1.03))
    self.assertTrue(feq(grd3.GetVal(50), 1.03))

    grd3 &= grd1
    self.assertTrue(feq(grd1.GetVal(50), 37.37))
    self.assertTrue(feq(grd3.GetVal(50), 1.03))

    grd2 &= grd4
    self.assertTrue(feq(grd2.GetVal(50), 1.03))
    self.assertTrue(feq(grd4.GetVal(50), 1.03))

    grd4 &= grd1
    self.assertTrue(feq(grd1.GetVal(50), 37.37))
    self.assertTrue(feq(grd4.GetVal(50), 1.03))

    grd1 += grd2
    self.assertTrue(feq(grd1.GetVal(50), 38.40))
    self.assertTrue(feq(grd2.GetVal(50), 1.03))

    grd1 -= grd2
    self.assertTrue(feq(grd1.GetVal(50), 37.37))
    self.assertTrue(feq(grd2.GetVal(50), 1.03))

    grd2 -= grd1
    self.assertTrue(feq(grd1.GetVal(50), 37.37))
    self.assertTrue(feq(grd2.GetVal(50), -36.34))

  def test10Dihedrals(self):
    p1 = geom.Point3D(1, 0, 0)
    p2 = geom.Point3D(0, 0, 0)
    p3 = geom.Point3D(0, 1, 0)

    p4 = geom.Point3D(.5, 1, .5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, -math.pi / 4, 4)

    p4 = geom.Point3D(-.5, 1, .5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 3 * math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, -3 * math.pi / 4, 4)

    p4 = geom.Point3D(.5, 1, -.5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 4, 4)

    p4 = geom.Point3D(-.5, 1, -.5)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 3 * math.pi / 4, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 3 * math.pi / 4, 4)

    p4 = geom.Point3D(0, 1, 1)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 2, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, -math.pi / 2, 4)

    p4 = geom.Point3D(0, 1, -1)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 2, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi / 2, 4)

    p4 = geom.Point3D(1, 1, 0)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 0, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, 0, 4)

    p4 = geom.Point3D(-1, 1, 0)
    ang = geom.ComputeDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi, 4)
    ang = geom.ComputeSignedDihedralAngle(p1, p2, p3, p4)
    self.assertAlmostEqual(ang, math.pi, 4)

  def test11UniformGridIndices(self):
    ugrid = geom.UniformGrid3D(20, 18, 15)
    idx = ugrid.GetGridIndex(3, 2, 1)
    xi, yi, zi = ugrid.GetGridIndices(idx)
    self.assertEqual(xi, 3)
    self.assertEqual(yi, 2)
    self.assertEqual(zi, 1)

  def test12UniformRealGridIndices(self):
    ugrid = geom.UniformRealValueGrid3D(20, 18, 15)
    idx = ugrid.GetGridIndex(3, 2, 1)
    xi, yi, zi = ugrid.GetGridIndices(idx)
    self.assertEqual(xi, 3)
    self.assertEqual(yi, 2)
    self.assertEqual(zi, 1)

    pt = ugrid.GetOffset()
    ugrid.SetValPoint(pt, 2.3)
    idx = ugrid.GetGridPointIndex(pt)
    self.assertTrue(feq(ugrid.GetValPoint(pt), 2.3))
    self.assertTrue(idx == 0)
    self.assertTrue(feq(ugrid.GetVal(idx), 2.3))

    pt2 = ugrid.GetGridPointLoc(idx)
    self.assertTrue(feq(pt.x, pt2.x))
    self.assertTrue(feq(pt.y, pt2.y))
    self.assertTrue(feq(pt.z, pt2.z))


if __name__ == '__main__':
  print("Testing Geometry wrapper")
  unittest.main()
