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# Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
#
# $Id: testDepictor.py 2112 2012-07-02 09:47:45Z glandrum $
#
# pylint:disable=E1101,C0111,C0103,R0904
import unittest
import os
import sys
import numpy as np
from rdkit import Chem
from rdkit.Chem import rdDepictor, rdMolAlign
from rdkit import Geometry
from rdkit import RDConfig
from rdkit.Chem.ChemUtils import AlignDepict
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def ptEq(pt1, pt2, tol=1e-4):
return feq(pt1.x, pt2.x, tol) and feq(pt1.y, pt2.y, tol) and feq(pt1.z, pt2.z, tol)
def getDistMat(mol):
conf = mol.GetConformer()
nat = mol.GetNumAtoms()
nl = nat * (nat - 1) // 2
res = np.zeros(nl, np.float)
for i in range(1, nat):
pi = conf.GetAtomPosition(i)
idx = i * (i - 1) // 2
for j in range(i):
pj = conf.GetAtomPosition(j)
pj -= pi
res[idx + j] = pj.Length()
return res
def compareCoords(m, molFile):
mo = Chem.MolFromMolFile(molFile)
co = mo.GetConformer()
ci = m.GetConformer()
nat = m.GetNumAtoms()
if (nat != mo.GetNumAtoms()):
return 0
for i in range(nat):
pos = ci.GetAtomPosition(i)
opos = co.GetAtomPosition(i)
if not ptEq(pos, opos):
print(Chem.MolToMolBlock(m))
print(Chem.MolToMolBlock(mo))
return 0
return 1
def compareWithOld(smilesFile, sdFile):
smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
sdsup = Chem.SDMolSupplier(sdFile)
im = 0
for mol in smiSup:
omol = sdsup[im]
rdDepictor.Compute2DCoords(mol, canonOrient=False)
conf = mol.GetConformer()
oconf = omol.GetConformer()
nat = mol.GetNumAtoms()
for i in range(nat):
pos = conf.GetAtomPosition(i)
opos = oconf.GetAtomPosition(i)
if not ptEq(pos, opos):
print(Chem.MolToMolBlock(omol), file=sys.stderr)
print('> <Failed>\n%d\n' % i, file=sys.stderr)
print("$$$$", file=sys.stderr)
print(Chem.MolToMolBlock(mol), file=sys.stderr)
print('> <Failed>\n%d\n' % i, file=sys.stderr)
print("$$$$", file=sys.stderr)
return 0
im += 1
return 1
def stereoCompare(smilesFile):
smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
for mol in smiSup:
rdDepictor.Compute2DCoords(mol, canonOrient=False)
mb = Chem.MolToMolBlock(mol)
nmol = Chem.MolFromMolBlock(mb)
matches = nmol.GetSubstructMatches(mol, False)
dbnds = [x for x in mol.GetBonds() if (x.GetBondType() == Chem.BondType.DOUBLE and
x.GetStereo() > Chem.BondStereo.STEREOANY) ]
ok = True
for match in matches:
for bnd in dbnds:
obnd = nmol.GetBondBetweenAtoms(
match[bnd.GetBeginAtomIdx()], match[bnd.GetEndAtomIdx()])
assert (obnd.GetBondType() == Chem.BondType.DOUBLE)
if ok:
break
if not ok:
print(Chem.MolToMolBlock(mol), file=sys.stderr)
print("$$$$", file=sys.stderr)
return 0
return 1
class TestCase(unittest.TestCase):
def _test0First200(self):
# this test is disabled because it's not particularly useful and
# causes problems every time anything changes.
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
'first_200.tpsa.csv')
#smiSup = Chem.SmilesMolSupplier(fileN, ",", 0, -1)
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
'first_200.python.sdf')
self.assertTrue(compareWithOld(fileN, ofile))
def test1CisTrans(self):
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
"cis_trans_cases.csv")
self.assertTrue(stereoCompare(fileN))
def test2Coords(self):
m1 = Chem.MolFromSmiles('C1CCC1CC')
coordMap = {0: Geometry.Point2D(0, 0),
1: Geometry.Point2D(1.5, 0),
2: Geometry.Point2D(1.5, 1.5),
3: Geometry.Point2D(0, 1.5)}
rdDepictor.Compute2DCoords(m1, coordMap=coordMap)
conf = m1.GetConformer(0)
for i in range(4):
self.assertTrue(
ptEq(conf.GetAtomPosition(i), Geometry.Point3D(coordMap[i].x, coordMap[i].y, 0.0)))
m1 = Chem.MolFromSmiles('CCC')
try:
rdDepictor.Compute2DCoords(m1, coordMap=coordMap)
ok = 0
except ValueError:
ok = 1
self.assertTrue(ok)
def test3IssueSF1526844(self):
t = Chem.MolFromSmiles('c1nc(N)ccc1')
rdDepictor.Compute2DCoords(t, canonOrient=False)
m2 = Chem.MolFromSmiles('c1nc(NC=O)ccc1')
AlignDepict.AlignDepict(m2, t)
expected = [Geometry.Point3D(1.5, 0.0, 0.0), Geometry.Point3D(0.75, -1.299, 0.0),
Geometry.Point3D(-0.75, -1.299, 0.0), Geometry.Point3D(-1.5, -2.5981, 0.0),
Geometry.Point3D(-3.0, -2.5981, 0.0), Geometry.Point3D(-3.75, -3.8971, 0.0),
Geometry.Point3D(-1.5, 0.0, 0.0), Geometry.Point3D(-0.75, 1.2990, 0.0),
Geometry.Point3D(0.75, 1.2990, 0.0)]
nat = m2.GetNumAtoms()
conf = m2.GetConformer()
for i in range(nat):
pos = conf.GetAtomPosition(i)
self.assertTrue(ptEq(pos, expected[i], 0.001))
def test4SamplingSpread(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor', 'test_data/7UPJ_xtal.mol'))
# default mode
rdDepictor.Compute2DCoords(mol, canonOrient=False)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_default.mol')))
# spread the structure as much as possible by sampling
rdDepictor.Compute2DCoords(mol, canonOrient=False, nFlipsPerSample=3, nSample=100,
sampleSeed=100, permuteDeg4Nodes=1)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_spread.mol')))
def test5SamplingMimic3D(self):
mol = Chem.MolFromMolFile(
os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor', 'test_data/7UPJ_xtal.mol'))
dmat3D = getDistMat(mol)
# now mimic the coordinate with a very small weight
rdDepictor.Compute2DCoordsMimicDistmat(mol, dmat3D, weightDistMat=0.001)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_mimic3D_1.mol')))
# now mimic the coordinate with a very small weight
rdDepictor.Compute2DCoordsMimicDistmat(mol, dmat3D, weightDistMat=0.003)
self.assertTrue(
compareCoords(mol, os.path.join(RDConfig.RDBaseDir, 'Code/GraphMol/Depictor',
'test_data/7UPJ_mimic3D_2.mol')))
#mb = Chem.MolToMolBlock(mol)
#ofile = open('../test_data/7UPJ_mimic3D_2.mol', 'w')
# ofile.write(mb)
# ofile.close()
def test6ChangeBondLength(self):
m = Chem.MolFromSmiles('CC')
rdDepictor.Compute2DCoords(m)
conf = m.GetConformer()
self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.750, 3)
self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.750, 3)
rdDepictor.Compute2DCoords(m, bondLength=1.0)
conf = m.GetConformer()
self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.500, 3)
self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.500, 3)
rdDepictor.Compute2DCoords(m)
conf = m.GetConformer()
self.assertAlmostEqual(conf.GetAtomPosition(0).x, -0.750, 3)
self.assertAlmostEqual(conf.GetAtomPosition(1).x, 0.750, 3)
def testConstrainedCoords(self):
templ = Chem.MolFromSmiles('c1nccc2n1ccc2')
rdDepictor.Compute2DCoords(templ)
m1 = Chem.MolFromSmiles('c1cccc2ncn3cccc3c21')
rdDepictor.GenerateDepictionMatching2DStructure(m1, templ)
m2 = Chem.MolFromSmiles('c1cc(Cl)cc2ncn3cccc3c21')
rdDepictor.Compute2DCoords(m2)
refPatt1 = Chem.MolFromSmarts('*1****2*1***2')
rdDepictor.GenerateDepictionMatching2DStructure(m2, templ, -1, refPatt1)
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Depictor', 'test_data',
'1XP0_ligand.sdf')
xp0_lig = Chem.MolFromMolFile(fileN)
xp0_lig_2d = Chem.Mol(xp0_lig)
rdDepictor.GenerateDepictionMatching3DStructure(xp0_lig_2d, xp0_lig)
xp0_ref = Chem.MolFromSmarts('[#6]1~[#7][#6]~[#6]2[#6](=[#8])[#7]~[#6](c3ccccc3)[#7][#7]12')
rdDepictor.GenerateDepictionMatching3DStructure(xp0_lig_2d, xp0_lig, -1, xp0_ref)
def testGenerate2DDepictionRefPatternAtomMap(self):
indazoleMolblock = """
RDKit 2D
9 10 0 0 0 0 0 0 0 0999 V2000
-6.0878 2.4335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.3867 1.6835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.3867 0.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.0878 -0.5666 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7887 0.1833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.7887 1.6835 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4897 -0.5664 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1906 1.6833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1906 0.1835 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
8 9 2 0
6 8 1 0
7 9 1 0
7 5 1 0
M END"""
indazoleRef = Chem.MolFromMolBlock(indazoleMolblock)
cycloheptylPyrazole = Chem.MolFromSmiles("c1cc(C2CCCCCC2)[nH]n1")
# test using refPattern
refPatt = Chem.MolFromSmarts("a1aan[nH]1")
rdDepictor.GenerateDepictionMatching2DStructure(cycloheptylPyrazole, indazoleRef, refPatt=refPatt)
self.assertEqual(cycloheptylPyrazole.GetNumConformers(), 1)
molMatchVect = cycloheptylPyrazole.GetSubstructMatch(refPatt)
self.assertEqual(len(molMatchVect), refPatt.GetNumAtoms())
refMatchVect = indazoleRef.GetSubstructMatch(refPatt)
self.assertEqual(len(refMatchVect), refPatt.GetNumAtoms())
atomMap = tuple(zip(refMatchVect, molMatchVect))
msd = 0.0
for refIdx, molIdx in atomMap:
msd += (indazoleRef.GetConformer().GetAtomPosition(refIdx) -
cycloheptylPyrazole.GetConformer().GetAtomPosition(molIdx)).LengthSq()
msd /= len(molMatchVect)
self.assertAlmostEqual(msd, 0.0)
# try with a pattern larger than the reference molecule
hugePatt = Chem.MolFromSmarts("CCCCCCCCCCCCCCCCCCCCCCCCCCC")
with self.assertRaises(ValueError):
rdDepictor.GenerateDepictionMatching2DStructure(
cycloheptylPyrazole, indazoleRef, refPatt=hugePatt)
# try with an out of range confId
with self.assertRaises(ValueError):
rdDepictor.GenerateDepictionMatching2DStructure(
cycloheptylPyrazole, indazoleRef, confId=1, refPatt=refPatt)
# test using atomMap directly
cycloheptylPyrazole.RemoveAllConformers()
rdDepictor.GenerateDepictionMatching2DStructure(cycloheptylPyrazole, indazoleRef, atomMap=atomMap)
self.assertEqual(cycloheptylPyrazole.GetNumConformers(), 1)
msd = 0.0
for refIdx, molIdx in atomMap:
msd += (indazoleRef.GetConformer().GetAtomPosition(refIdx) -
cycloheptylPyrazole.GetConformer().GetAtomPosition(molIdx)).LengthSq()
msd /= len(atomMap)
self.assertAlmostEqual(msd, 0.0)
# try with an atomMap larger than the reference molecule
atomMapHuge = list(atomMap) + [(0, 0) for i in range(indazoleRef.GetNumAtoms())]
with self.assertRaises(ValueError):
rdDepictor.GenerateDepictionMatching2DStructure(
cycloheptylPyrazole, indazoleRef, atomMap=atomMapHuge)
# try with an atomMap with out of range indices
atomMapOutOfRange = list(atomMap) + [(100, 100)]
with self.assertRaises(ValueError):
rdDepictor.GenerateDepictionMatching2DStructure(
cycloheptylPyrazole, indazoleRef, atomMap=atomMapOutOfRange)
# try with an out of range confId
with self.assertRaises(ValueError):
rdDepictor.GenerateDepictionMatching2DStructure(
cycloheptylPyrazole, indazoleRef, atomMap=atomMap, confId=1)
def testGenerate2DDepictionAllowRGroups(self):
templateMolblock = """
RDKit 2D
9 9 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 1.0942 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1.7051 1.0942 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
-3.4910 -1.9059 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
6 8 1 0
3 9 1 0
2 7 1 0
M RGP 3 7 1 8 2 9 3
M END"""
templateRef = Chem.MolFromMolBlock(templateMolblock)
orthoMeta = Chem.MolFromSmiles("c1ccc(-c2ccc(-c3ccccc3)c(-c3ccccc3)c2)cc1")
ortho = Chem.MolFromSmiles("c1ccc(-c2ccccc2-c2ccccc2)cc1")
meta = Chem.MolFromSmiles("c1ccc(-c2cccc(-c3ccccc3)c2)cc1")
biphenyl = Chem.MolFromSmiles("c1ccccc1-c1ccccc1")
phenyl = Chem.MolFromSmiles("c1ccccc1")
atomMap = rdDepictor.GenerateDepictionMatching2DStructure(orthoMeta, templateRef)
self.assertEqual(orthoMeta.GetNumConformers(), 1)
for mol in (ortho, meta, biphenyl, phenyl):
# fails as does not match template
with self.assertRaises(ValueError):
rdDepictor.GenerateDepictionMatching2DStructure(mol, templateRef)
# succeeds with allowRGroups=true
atomMap = rdDepictor.GenerateDepictionMatching2DStructure(mol, templateRef, allowRGroups=True)
self.assertEqual(mol.GetNumConformers(), 1)
msd = 0.0
for refIdx, molIdx in atomMap:
msd += (templateRef.GetConformer().GetAtomPosition(refIdx) -
mol.GetConformer().GetAtomPosition(molIdx)).LengthSq()
msd /= len(atomMap)
self.assertAlmostEqual(msd, 0.0)
# test that using a refPattern with R groups and a reference without works
pyridineRef = Chem.MolFromMolBlock("""
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
-0.8929 1.0942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 0.3442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1919 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8929 -1.9059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 -1.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4060 0.3442 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END""")
genericRefPatternWithRGroups = Chem.MolFromSmarts("[*:3]a1a([*:1])aa([*:2])aa1")
for mol in (ortho, meta, biphenyl, phenyl):
atomMap = rdDepictor.GenerateDepictionMatching2DStructure(
mol, pyridineRef, refPatt=genericRefPatternWithRGroups, allowRGroups=True)
self.assertEqual(mol.GetNumConformers(), 1)
msd = 0.0
for refIdx, molIdx in atomMap:
msd += (pyridineRef.GetConformer().GetAtomPosition(refIdx) -
mol.GetConformer().GetAtomPosition(molIdx)).LengthSq()
msd /= len(atomMap)
self.assertAlmostEqual(msd, 0.0)
def testNormalizeStraighten(self):
noradrenalineMJ = Chem.MolFromMolBlock("""
MJ201100
12 12 0 0 1 0 0 0 0 0999 V2000
2.2687 1.0716 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.4437 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0312 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4437 -0.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.2062 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2062 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0312 -0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4437 -1.0716 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.4437 0.3572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2687 0.3572 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.0312 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2062 1.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
3 2 1 0 0 0 0
3 4 1 6 0 0 0
3 5 1 0 0 0 0
5 6 2 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
9 10 1 0 0 0 0
9 11 1 0 0 0 0
11 12 2 0 0 0 0
5 12 1 0 0 0 0
M END)""")
noradrenalineMJCopy = Chem.Mol(noradrenalineMJ)
conformer0 = noradrenalineMJCopy.GetConformer(0)
conformer1 = Chem.Conformer(conformer0)
noradrenalineMJCopy.AddConformer(conformer1, True)
conformer1 = noradrenalineMJCopy.GetConformer(1)
self.assertLess(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 0), 1.e-5)
self.assertLess(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 1), 1.e-5)
scalingFactor = rdDepictor.NormalizeDepiction(noradrenalineMJCopy, 1)
self.assertLess(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 0), 1.e-5)
self.assertGreater(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 1), 1.e-5)
self.assertAlmostEqual(scalingFactor, 1.875, 3)
conformer2 = Chem.Conformer(conformer1)
noradrenalineMJCopy.AddConformer(conformer2, True)
conformer2 = noradrenalineMJCopy.GetConformer(2)
bond10_11Conf0 = conformer0.GetAtomPosition(11) - conformer0.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf0.x, 0.825, 3)
self.assertAlmostEqual(bond10_11Conf0.y, 0., 3)
bond10_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf1.x, 1.513, 3)
self.assertAlmostEqual(bond10_11Conf1.y, -0.321, 3)
rdDepictor.StraightenDepiction(noradrenalineMJCopy, 1)
bond10_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf1.x, 1.340, 3)
self.assertAlmostEqual(bond10_11Conf1.y, -0.773, 3)
bond4_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(4)
self.assertAlmostEqual(bond4_11Conf1.x, 0., 3)
self.assertAlmostEqual(bond4_11Conf1.y, 1.547, 3)
rdDepictor.StraightenDepiction(noradrenalineMJCopy, 2, True)
bond10_11Conf2 = conformer2.GetAtomPosition(11) - conformer2.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf2.x, 1.547, 3)
self.assertAlmostEqual(bond10_11Conf2.y, 0.0, 3)
bond4_11Conf2 = conformer2.GetAtomPosition(11) - conformer2.GetAtomPosition(4)
self.assertAlmostEqual(bond4_11Conf2.x, -0.773, 3)
self.assertAlmostEqual(bond4_11Conf2.y, 1.339, 3)
noradrenalineMJCopy = Chem.Mol(noradrenalineMJ)
conformer0 = noradrenalineMJCopy.GetConformer(0)
conformer1 = Chem.Conformer(conformer0)
noradrenalineMJCopy.AddConformer(conformer1, True)
conformer1 = noradrenalineMJCopy.GetConformer(1)
scalingFactor = rdDepictor.NormalizeDepiction(noradrenalineMJCopy, 1, -1)
self.assertLess(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 0), 1.e-5)
self.assertGreater(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 1), 1.e-5)
self.assertAlmostEqual(scalingFactor, 1.875, 3)
conformer2 = Chem.Conformer(conformer1)
noradrenalineMJCopy.AddConformer(conformer2, True)
conformer2 = noradrenalineMJCopy.GetConformer(2)
bond10_11Conf0 = conformer0.GetAtomPosition(11) - conformer0.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf0.x, 0.825, 3)
self.assertAlmostEqual(bond10_11Conf0.y, 0., 3)
bond10_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf1.x, 0.321, 3)
self.assertAlmostEqual(bond10_11Conf1.y, 1.513, 3)
rdDepictor.StraightenDepiction(noradrenalineMJCopy, 1)
bond10_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf1.x, 0.0, 3)
self.assertAlmostEqual(bond10_11Conf1.y, 1.547, 3)
rdDepictor.StraightenDepiction(noradrenalineMJCopy, 2, True)
bond10_11Conf2 = conformer2.GetAtomPosition(11) - conformer2.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf2.x, bond10_11Conf1.x, 3)
self.assertAlmostEqual(bond10_11Conf2.y, bond10_11Conf1.y, 3)
noradrenalineMJCopy = Chem.Mol(noradrenalineMJ)
conformer0 = noradrenalineMJCopy.GetConformer(0)
conformer1 = Chem.Conformer(conformer0)
noradrenalineMJCopy.AddConformer(conformer1, True)
conformer1 = noradrenalineMJCopy.GetConformer(1)
scalingFactor = rdDepictor.NormalizeDepiction(noradrenalineMJCopy, 1, 0, 3.0)
self.assertLess(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 0), 1.e-5)
self.assertGreater(rdMolAlign.CalcRMS(noradrenalineMJ, noradrenalineMJCopy, 0, 1), 1.e-5)
self.assertAlmostEqual(scalingFactor, 3.0, 3)
conformer2 = Chem.Conformer(conformer1)
noradrenalineMJCopy.AddConformer(conformer2, True)
conformer2 = noradrenalineMJCopy.GetConformer(2)
conformer3 = Chem.Conformer(conformer1)
noradrenalineMJCopy.AddConformer(conformer3, True)
conformer3 = noradrenalineMJCopy.GetConformer(3)
bond10_11Conf0 = conformer0.GetAtomPosition(11) - conformer0.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf0.x, 0.825, 3)
self.assertAlmostEqual(bond10_11Conf0.y, 0., 3)
bond10_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf1.x, 2.475, 3)
self.assertAlmostEqual(bond10_11Conf1.y, 0., 3)
rdDepictor.StraightenDepiction(noradrenalineMJCopy, 1)
bond10_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf1.x, 2.143, 3)
self.assertAlmostEqual(bond10_11Conf1.y, -1.237, 3)
bond4_11Conf1 = conformer1.GetAtomPosition(11) - conformer1.GetAtomPosition(4)
self.assertAlmostEqual(bond4_11Conf1.x, 0., 3)
self.assertAlmostEqual(bond4_11Conf1.y, 2.475, 3)
rdDepictor.StraightenDepiction(noradrenalineMJCopy, 2, True)
bond10_11Conf2 = conformer2.GetAtomPosition(11) - conformer2.GetAtomPosition(10)
bond10_11Conf3 = conformer3.GetAtomPosition(11) - conformer3.GetAtomPosition(10)
self.assertAlmostEqual(bond10_11Conf2.x, bond10_11Conf3.x, 3)
self.assertAlmostEqual(bond10_11Conf2.y, bond10_11Conf3.y, 3)
bond4_11Conf2 = conformer2.GetAtomPosition(11) - conformer2.GetAtomPosition(4)
bond4_11Conf3 = conformer3.GetAtomPosition(11) - conformer3.GetAtomPosition(4)
self.assertAlmostEqual(bond4_11Conf2.x, bond4_11Conf3.x, 3)
self.assertAlmostEqual(bond4_11Conf2.y, bond4_11Conf3.y, 3)
if __name__ == '__main__':
rdDepictor.SetPreferCoordGen(False)
unittest.main()
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