from __future__ import print_function
import unittest
import os, copy
import math
import numpy

from rdkit.six.moves import cPickle as pickle
from rdkit.six import next
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdDistGeom, ChemicalForceFields, rdMolAlign
from rdkit import RDConfig, rdBase
from rdkit.Geometry import rdGeometry as geom
from rdkit.RDLogger import logger
logger = logger()


def feq(v1, v2, tol=1.e-4):
  return abs(v1 - v2) < tol


def lstEq(l1, l2, tol=1.0e-4):
  ln = len(l1)
  if (ln != len(l2)):
    return 0

  for i in range(ln):
    if abs(l1[i] - l2[i]) > tol:
      return 0
  return 1


def compareWithOld(smilesFile, sdFile):
  smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
  sdsup = Chem.SDMolSupplier(sdFile)
  im = 0
  for mol in smiSup:
    cid = rdDistGeom.EmbedMolecule(mol, 10, 1)
    omol = sdsup[im]
    assert cid == 0
    conf = mol.GetConformer(0)
    oconf = omol.GetConformer()
    nat = mol.GetNumAtoms()
    for i in range(nat):
      #atm = mol.GetAtomWithIdx(i)
      #oatm = omol.GetAtomWithIdx(i)
      pos = conf.GetAtomPosition(i)
      opos = oconf.GetAtomPosition(i)
      if not lstEq(pos, opos):
        return 0
    im += 1
  return 1


def compareMatrices(bm1, bm2, map, tol=1.0e-5):
  N = numpy.shape(bm1)[0]
  for i in range(1, N):
    for j in range(i):
      l, m = map[i], map[j]
      if (l < m):
        l, m = m, l
      if (abs(bm1[l, m] - bm2[i, j]) > tol):
        return 0

      if (abs(bm1[m, l] - bm2[j, i]) > tol):
        return 0

  return 1


def compareOrder(smi1, smi2, tol=1.0e-5):
  m1 = Chem.MolFromSmiles(smi1)
  m2 = Chem.MolFromSmiles(smi2)
  bm1 = rdDistGeom.GetMoleculeBoundsMatrix(m1)
  bm2 = rdDistGeom.GetMoleculeBoundsMatrix(m2)
  map = m1.GetSubstructMatch(m2)
  return compareMatrices(bm1, bm2, map, tol)


def computeDist(lst1, lst2):
  res = 0.0
  for i, val in enumerate(lst1):
    res += (val - lst2[i]) * (val - lst2[i])
  res = math.sqrt(res)
  return res


def computeChiralVol(pt1, pt2, pt3, pt4):
  v1 = pt1 - pt4
  v2 = pt2 - pt4
  v3 = pt3 - pt4
  cp = v2.CrossProduct(v3)
  vol = v1.DotProduct(cp)
  return vol


class TestCase(unittest.TestCase):

  def setUp(self):
    pass

  def _test0Cdk2(self):
    fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                         'cis_trans_cases.csv')

    ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                         'embedDistOpti.sdf')
    self.assertTrue(compareWithOld(fileN, ofile))

  def test1Small(self):
    #writer = Chem.SDWriter("test.sdf")
    # single double and tripple atoms cases should not fail
    mol = Chem.MolFromSmiles('O')
    rdDistGeom.EmbedMolecule(mol, 10, 1)
    conf = mol.GetConformer()
    self.assertTrue(lstEq(conf.GetAtomPosition(0), [0.0, 0.0, 0.0]))
    #writer.write(mol)

    mol = Chem.MolFromSmiles('CO')
    rdDistGeom.EmbedMolecule(mol, 10, 1)
    conf = mol.GetConformer()
    self.assertTrue(lstEq(conf.GetAtomPosition(0), [0.69192, 0.0, 0.0]))
    self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.69192, 0.0, 0.0]))
    #writer.write(mol)

    mol = Chem.MolFromSmiles('CCC')
    rdDistGeom.EmbedMolecule(mol, 10, 1)
    conf = mol.GetConformer()
    self.assertTrue(lstEq(conf.GetAtomPosition(0), [-1.21676, -0.2989, 0.0]))
    self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.00604, 0.59337, 0.0]))
    self.assertTrue(lstEq(conf.GetAtomPosition(2), [1.22281, -0.29446, 0.0]))
    #writer.write(mol)

    mol = Chem.MolFromSmiles('O=C=O')
    rdDistGeom.EmbedMolecule(mol, 10, 1)
    conf = mol.GetConformer()

    #writer.write(mol)
    self.assertTrue(lstEq(conf.GetAtomPosition(0), [-1.2180, -0.06088, 0.0]))
    self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.00408, 0.12116, 0.0]))
    self.assertTrue(lstEq(conf.GetAtomPosition(2), [1.22207, -0.060276, 0.0]))

    mol = Chem.MolFromSmiles('C=C=C=C')
    rdDistGeom.EmbedMolecule(mol, 10, 1, useExpTorsionAnglePrefs=False,
                             useBasicKnowledge=False)
    conf = mol.GetConformer()

    #writer.write(mol)

    d1 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(1))
    self.assertTrue(feq(d1, 1.31, 0.01))
    d2 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(2))
    self.assertTrue(feq(d2, 2.59, 0.05))
    d3 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(3))
    self.assertTrue(feq(d3, 3.84, 0.1))
    d4 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(2))
    self.assertTrue(feq(d4, 1.29, 0.01))
    d5 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(3))
    self.assertTrue(feq(d5, 2.54, 0.1))
    d6 = computeDist(conf.GetAtomPosition(2), conf.GetAtomPosition(3))
    self.assertTrue(feq(d6, 1.31, 0.01))

  def test2Utils(self):
    mol = Chem.MolFromSmiles('CC')
    bm = rdDistGeom.GetMoleculeBoundsMatrix(mol)
    self.assertTrue(bm[1, 0] > 0)
    self.assertTrue(bm[0, 1] > 0)
    self.assertTrue(bm[0, 1] >= bm[1, 0])
    self.assertTrue(bm[1, 0] < 1.510)
    self.assertTrue(bm[0, 1] > 1.510)

  def test3MultiConf(self):
    mol = Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC")
    cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30, randomSeed=100,
                             useExpTorsionAnglePrefs=False,
                             useBasicKnowledge=False)
    energies = [112.98, 103.57, 110.78, 100.40, 95.37, 101.64, 114.72, 112.65, 124.53, 107.50]
    nenergies = []
    for cid in cids:
      ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
      ee = ff.CalcEnergy()
      nenergies.append(ee)
    #print(['%.2f'%x for x in nenergies])
    #print(nenergies)
    self.assertTrue(lstEq(energies, nenergies, tol=1e-2))

  def test4OrderDependence(self):
    self.assertTrue(
      compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12", "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
    #issue 230
    self.assertTrue(compareOrder("C#CC(C)(C)N(CN1)C\\N=C/1SC", "CSC1=NCN(C(C)(C)C#C)CN1"))
    #issue 232
    self.assertTrue(
      compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12", "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))

  def test5Issue285(self):
    m = Chem.MolFromSmiles('CNC=O')
    cs = rdDistGeom.EmbedMultipleConfs(m, 10)
    for i, ci in enumerate(cs):
      for j in range(i + 1, len(cs)):
        cj = cs[j]
        self.assertTrue(Chem.MolToMolBlock(m, confId=ci) != Chem.MolToMolBlock(m, confId=cj))

  def test6RmsPruning(self):
    smiles = [
      'CC(C)CC(NC(C1[N+]CCC1)=O)C([O-])=O', 'CC(NC(CO)C(O)c1ccc([N+]([O-])=O)cc1)=O',
      'CC([N+])C(NC(C)C(N1C(C=O)CCC1)=O)=O', 'CC(NC1C(O)C=C(C([O-])=O)OC1C(O)C(O)CO)=O',
      'CCCC=C(NC(C1CC1(C)C)=O)C([O-])=O', 'OCC(O)C(O)C(Cn1c2c(cc(C)c(C)c2)nc-2c(=O)[nH]c(=O)nc12)O'
    ]

    nconfs = []
    expected = [5, 6, 6, 6, 6, 3]
    for smi in smiles:
      mol = Chem.MolFromSmiles(smi)
      cids = rdDistGeom.EmbedMultipleConfs(mol, 50, maxAttempts=30, randomSeed=100,
                                           pruneRmsThresh=1.5)
      nconfs.append(len(cids))

    d = [abs(x - y) for x, y in zip(expected, nconfs)]

    self.assertTrue(max(d) <= 1)

  def test6Chirality(self):
    # turn on chirality and we should get chiral volume that is pretty consistent and
    # positive
    tgtVol = 13.0
    smiles = "Cl[C@](C)(F)Br"
    mol = Chem.MolFromSmiles(smiles)
    cids = rdDistGeom.EmbedMultipleConfs(mol, 30, maxAttempts=30, randomSeed=100)
    self.assertTrue(len(cids) == 30)
    for cid in cids:
      conf = mol.GetConformer(cid)
      vol = computeChiralVol(
        conf.GetAtomPosition(0),
        conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
      self.assertTrue(abs(vol - tgtVol) < 1)

    # turn of chirality and now we should see both chiral forms
    smiles = "ClC(C)(F)Br"
    mol = Chem.MolFromSmiles(smiles)
    cids = rdDistGeom.EmbedMultipleConfs(mol, 30, maxAttempts=30, randomSeed=120)
    self.assertTrue(len(cids) == 30)
    nPos = 0
    nNeg = 0
    for cid in cids:
      conf = mol.GetConformer(cid)
      vol = computeChiralVol(
        conf.GetAtomPosition(0),
        conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
      self.assertTrue(abs(vol - tgtVol) < 1 or abs(vol + tgtVol) < 1)
      if vol < 0:
        nNeg += 1
      else:
        nPos += 1
    self.assertTrue(nPos > 0)
    self.assertTrue(nNeg > 0)

    tgtVol = 5.0
    for i in range(10):
      smiles = "Cl[C@H](F)Br"
      mol = Chem.MolFromSmiles(smiles)
      ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
      conf = mol.GetConformer(ci)
      vol = computeChiralVol(
        conf.GetAtomPosition(0),
        conf.GetAtomPosition(1), conf.GetAtomPosition(2), conf.GetAtomPosition(3))
      self.assertTrue(abs(vol - tgtVol) < 1, "%s %s" % (vol, tgtVol))

    tgtVol = 3.5
    expected = [-3.62, -3.67, -3.72, 3.91, 3.95, 3.98, 3.90, 3.94, 3.98, 3.91]
    nPos = 0
    nNeg = 0
    for i in range(30):
      smiles = "ClC(F)Br"
      mol = Chem.MolFromSmiles(smiles)
      ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
      conf = mol.GetConformer(ci)
      vol = computeChiralVol(
        conf.GetAtomPosition(0),
        conf.GetAtomPosition(1), conf.GetAtomPosition(2), conf.GetAtomPosition(3))
      self.assertTrue(abs(vol - tgtVol) < 1 or abs(vol + tgtVol) < 1)
      if vol < 0:
        nNeg += 1
      else:
        nPos += 1

    self.assertTrue(nPos > 0)
    self.assertTrue(nNeg > 0)

    smiles = "Cl[C@H](F)Br"
    m = Chem.MolFromSmiles(smiles)
    mol = Chem.AddHs(m)
    cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30, randomSeed=100)
    self.assertTrue(len(cids) == 10)
    tgtVol = 10.5
    for cid in cids:
      conf = mol.GetConformer(cid)
      vol = computeChiralVol(
        conf.GetAtomPosition(0),
        conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
      self.assertTrue(abs(vol - tgtVol) < 2.)

    # let's try a little more complicated system
    expectedV1 = -2.0
    expectedV2 = -2.9

    for i in range(5):
      smi = "C1=CC=C(C=C1)[C@H](OC1=C[NH]N=C1)C(=O)[NH]C[C@H](Cl)C1=CC=NC=C1"
      mol = Chem.MolFromSmiles(smi)
      ci = rdDistGeom.EmbedMolecule(mol, randomSeed=(i + 1) * 15)
      self.assertTrue(ci >= 0)
      ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
      ff.Minimize()

      conf = mol.GetConformer(ci)
      vol1 = computeChiralVol(
        conf.GetAtomPosition(6),
        conf.GetAtomPosition(3), conf.GetAtomPosition(7), conf.GetAtomPosition(13))
      self.assertTrue(abs(vol1 - expectedV1) < 1 or abs(vol1 + expectedV1) < 1)
      if vol1 < 0:
        nNeg += 1
      else:
        nPos += 1

      vol2 = computeChiralVol(
        conf.GetAtomPosition(17),
        conf.GetAtomPosition(16), conf.GetAtomPosition(18), conf.GetAtomPosition(19))
      self.assertTrue(abs(vol2 - expectedV2) < 1 or abs(vol2 + expectedV2) < 1)

    # remove the chiral specification and we should see other chiral
    # forms of the compound
    expectedV1 = 2.0  #[-2.30, -2.31, -2.30,  2.30, -1.77]
    expectedV2 = 2.8  #[2.90,  2.89,  2.69, -2.90, -2.93]

    self.assertTrue(nPos > 0)
    self.assertTrue(nNeg > 0)
    for i in range(5):
      smi = "C1=CC=C(C=C1)C(OC1=C[NH]N=C1)C(=O)[NH]CC(Cl)C1=CC=NC=C1"
      mol = Chem.MolFromSmiles(smi)
      ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
      ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
      ff.Minimize()

      conf = mol.GetConformer(ci)
      vol1 = computeChiralVol(
        conf.GetAtomPosition(6),
        conf.GetAtomPosition(3), conf.GetAtomPosition(7), conf.GetAtomPosition(13))
      vol2 = computeChiralVol(
        conf.GetAtomPosition(17),
        conf.GetAtomPosition(16), conf.GetAtomPosition(18), conf.GetAtomPosition(19))
      self.assertTrue(abs(abs(vol1) - expectedV1) < 1.0)
      self.assertTrue(abs(abs(vol2) - expectedV2) < 1.0)

  def test7ConstrainedEmbedding(self):
    ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                         'constrain1.sdf')
    suppl = Chem.SDMolSupplier(ofile)
    ref = next(suppl)
    probe = copy.deepcopy(ref)

    cMap = {}
    for i in range(5):
      cMap[i] = ref.GetConformer().GetAtomPosition(i)
    ci = rdDistGeom.EmbedMolecule(probe, coordMap=cMap, randomSeed=23)
    self.assertTrue(ci > -1)
    algMap = list(zip(range(5), range(5)))
    ssd = rdMolAlign.AlignMol(probe, ref, atomMap=algMap)
    self.assertTrue(ssd < 0.1)

  def test8MultiThreadMultiConf(self):
    if (rdBase.rdkitBuild.split('|')[2] != "MINGW"):
      ENERGY_TOLERANCE = 1.0e-6
      MSD_TOLERANCE = 1.0e-6
    else:
      ENERGY_TOLERANCE = 1.0
      MSD_TOLERANCE = 1.0e-5
    mol = Chem.AddHs(Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC"))
    cids = rdDistGeom.EmbedMultipleConfs(mol, 200, maxAttempts=30, randomSeed=100)
    energies = []
    for cid in cids:
      ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
      ee = ff.CalcEnergy()
      energies.append(ee)

    mol2 = Chem.AddHs(Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC"))
    cids2 = rdDistGeom.EmbedMultipleConfs(mol2, 200, maxAttempts=30, randomSeed=100, numThreads=4)
    self.assertTrue(lstEq(cids, cids2))
    nenergies = []
    for cid in cids2:
      ff = ChemicalForceFields.UFFGetMoleculeForceField(mol2, 10.0, cid)
      ee = ff.CalcEnergy()
      nenergies.append(ee)

    self.assertTrue(lstEq(energies, nenergies, tol=ENERGY_TOLERANCE))

    for cid in cids:
      msd = 0.0
      for i in range(mol.GetNumAtoms()):
        msd += (mol.GetConformer().GetAtomPosition(i) \
            - mol2.GetConformer().GetAtomPosition(i)).LengthSq()
      msd /= mol.GetNumAtoms()
      self.assertTrue(msd < MSD_TOLERANCE)

  def _compareConfs(self, mol, ref, molConfId, refConfId):
    self.assertEqual(mol.GetNumAtoms(), ref.GetNumAtoms())
    molConf = mol.GetConformer(molConfId)
    refConf = ref.GetConformer(refConfId)
    for i in range(mol.GetNumAtoms()):
      mp = molConf.GetAtomPosition(i)
      rp = refConf.GetAtomPosition(i)
      self.assertAlmostEqual((mp - rp).Length(), 0.0, 3)

  def test9EmbedParams(self):
    mol = Chem.AddHs(Chem.MolFromSmiles('OCCC'))
    fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                      'simple_torsion.dg.mol')
    ref = Chem.MolFromMolFile(fn, removeHs=False)
    params = rdDistGeom.EmbedParameters()
    params.randomSeed = 42
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)

    fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                      'simple_torsion.etdg.mol')
    ref = Chem.MolFromMolFile(fn, removeHs=False)
    params = rdDistGeom.EmbedParameters()
    params.randomSeed = 42
    params.useExpTorsionAnglePrefs = True
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)
    params = rdDistGeom.ETDG()
    params.randomSeed = 42
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)

    fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                      'simple_torsion.etkdg.mol')
    ref = Chem.MolFromMolFile(fn, removeHs=False)
    params = rdDistGeom.EmbedParameters()
    params.randomSeed = 42
    params.useExpTorsionAnglePrefs = True
    params.useBasicKnowledge = True
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)
    params = rdDistGeom.ETKDG()
    params.randomSeed = 42
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)

    fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                      'simple_torsion.kdg.mol')
    ref = Chem.MolFromMolFile(fn, removeHs=False)
    params = rdDistGeom.EmbedParameters()
    params.randomSeed = 42
    params.useBasicKnowledge = True
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)
    params = rdDistGeom.KDG()
    params.randomSeed = 42
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)

  def test10ETKDGv2(self):
    mol = Chem.AddHs(Chem.MolFromSmiles('n1cccc(C)c1ON'))
    fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                      'torsion.etkdg.v2.mol')
    ref = Chem.MolFromMolFile(fn, removeHs=False)
    params = rdDistGeom.ETKDGv2()
    params.randomSeed = 42
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
    self._compareConfs(mol, ref, 0, 0)

  def assertDeterministicWithSeed(self, seed):
    input_mol = Chem.MolFromSmiles('CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)NC(CCC(=O)O)C(=O)O)cc1')

    params = AllChem.ETKDG()
    params.pruneRmsThresh = -1.0 # skip internal RMSD pruning
    if seed is not None:
      params.randomSeed = seed

    firstMol = Chem.AddHs(input_mol)
    firstIds = AllChem.EmbedMultipleConfs(firstMol, 11, params)

    secondMol = Chem.AddHs(input_mol)
    secondIds = AllChem.EmbedMultipleConfs(secondMol, 11, params)

    self.assertEqual(list(firstIds), list(secondIds))
    self.assertEqual(firstMol.GetNumConformers(), secondMol.GetNumConformers())

    nonDeterministic = False
    for confIdx in range(firstMol.GetNumConformers()):

      firstConf = firstMol.GetConformer(confIdx)
      secondConf = secondMol.GetConformer(confIdx)

      firstPositions = firstConf.GetPositions()
      secondPositions = secondConf.GetPositions()

      d = firstPositions - secondPositions
      rmsd = numpy.sqrt(numpy.sum(d * d))
      if seed >= 0:
        self.assertEquals(rmsd, 0.0)
      elif rmsd != 0.0:
        nonDeterministic = True
    if seed < 0:
      self.assertTrue(nonDeterministic)

  def testETKDGIsDeterministic(self):
    self.assertDeterministicWithSeed(-1) # not deterministic
    self.assertDeterministicWithSeed(0) # deterministic
    self.assertDeterministicWithSeed(1) # deterministic
    self.assertDeterministicWithSeed(195225786) # as large as we can go without overflowing since 11 * 195225786 should not overflow the int
    self.assertDeterministicWithSeed(195225787) # one higher seed will overflow though
    self.assertDeterministicWithSeed(0x1CEB00DA) # another large seeds that shouldn't overflow internals and make them non-deterministic

  def testGithub1763(self):
    mol = Chem.MolFromSmiles('CCCCC')
    bm1 = rdDistGeom.GetMoleculeBoundsMatrix(mol)
    bm2 = rdDistGeom.GetMoleculeBoundsMatrix(mol,doTriangleSmoothing=False)
    self.assertTrue(bm1[0, 4] < bm2[0,4])

  def testGithub2057(self):
      # ensure that ETKDG is the default Embedder
    mol = Chem.AddHs(Chem.MolFromSmiles('OCCC'))
    fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
                        'simple_torsion.etkdg.mol')
    ref = Chem.MolFromMolFile(fn, removeHs=False)
    self.assertEqual(rdDistGeom.EmbedMolecule(mol, randomSeed=42), 0)
    self._compareConfs(mol, ref, 0, 0)

if __name__ == '__main__':
  unittest.main()