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rdkit/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py

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from rdkit import RDConfig
import os, sys, math
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdMolTransforms as rdmt
def feq(v1, v2, tol=1.0e-4):
return abs(v1 - v2) < tol
def ptEq(pt, tpt, tol=0.0001):
pt -= tpt
return feq(pt.Length(), 0.0)
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1Canonicalization(self):
mol = Chem.MolFromSmiles("C")
conf = Chem.Conformer(1)
conf.SetAtomPosition(0, (4.0, 5.0, 6.0))
mol.AddConformer(conf, 1)
conf = mol.GetConformer()
pt = rdmt.ComputeCentroid(conf)
self.failUnless(ptEq(pt, geom.Point3D(4.0, 5.0, 6.0)))
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
'1oir.mol')
m = Chem.MolFromMolFile(fileN)
cpt = rdmt.ComputeCentroid(m.GetConformer())
trans = rdmt.ComputeCanonicalTransform(m.GetConformer(), cpt)
trans2 = rdmt.ComputeCanonicalTransform(m.GetConformer())
for i in range(4):
for j in range(4):
self.failUnless(feq(trans[i, j], trans2[i, j]))
rdmt.TransformConformer(m.GetConformer(), trans2)
m2 = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeConformer(m2.GetConformer())
nats = m.GetNumAtoms()
cnf1 = m.GetConformer()
cnf2 = m2.GetConformer()
for i in range(nats):
p1 = list(cnf1.GetAtomPosition(i))
p2 = list(cnf2.GetAtomPosition(i))
self.failUnless(feq(p1[0], p2[0]))
self.failUnless(feq(p1[1], p2[1]))
self.failUnless(feq(p1[2], p2[2]))
m3 = Chem.MolFromMolFile(fileN)
rdmt.CanonicalizeMol(m3)
cnf1 = m.GetConformer()
cnf2 = m3.GetConformer()
for i in range(nats):
p1 = list(cnf1.GetAtomPosition(i))
p2 = list(cnf2.GetAtomPosition(i))
self.failUnless(feq(p1[0], p2[0]))
self.failUnless(feq(p1[1], p2[1]))
self.failUnless(feq(p1[2], p2[2]))
def testComputePrincipalAxesAndMoments(self):
if (not hasattr(rdmt, 'ComputePrincipalAxesAndMoments')):
return
molBlock = '''\
RDKit 3D
4 3 0 0 0 0 0 0 0 0999 V2000
-0.1888 1.3224 -0.2048 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0790 0.1671 0.6070 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.3083 -0.8939 -0.2236 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1.5761 -0.5956 -0.1786 Br 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 6
2 3 1 0
2 4 1 0
M END
'''
axesRef = (
(-0.9997, -0.0246, 0.0009),
( 0.0246, -0.9981, 0.0559),
( 0.0004, -0.0559, -0.9984)
)
momentsRef = ( 3.4220, 4.7230, 7.1757)
m = Chem.MolFromMolBlock(molBlock)
axes, moments = rdmt.ComputePrincipalAxesAndMoments(m.GetConformer())
self.assertIsNotNone(axes)
self.assertIsNotNone(moments)
for y in range(3):
for x in range(3):
self.assertAlmostEqual(axes[y][x], axesRef[y][x], 3)
self.assertAlmostEqual(moments[y], momentsRef[y], 3)
failed = False
try:
axes, moments = rdmt.ComputePrincipalAxesAndMoments(m.GetConformer(), weights = (0.5, 0.5))
except:
failed = True
self.assertTrue(failed)
axesWeightedRef = (
(-0.9998, -0.0114, -0.0189),
(-0.0153, 0.9744, 0.2245),
( 0.0158, 0.2247, -0.9743)
)
momentsWeightedRef = ( 0.5496, 1.5559, 1.9361)
axesWeighted, momentsWeighted = rdmt.ComputePrincipalAxesAndMoments(
m.GetConformer(), weights = (0.1, 0.2, 0.3, 0.4))
self.assertIsNotNone(axesWeighted)
self.assertIsNotNone(momentsWeighted)
for y in range(3):
for x in range(3):
self.assertAlmostEqual(axesWeighted[y][x], axesWeightedRef[y][x], 3)
self.assertAlmostEqual(momentsWeighted[y], momentsWeightedRef[y], 3)
def testComputePrincipalAxesAndMomentsFromGyrationMatrix(self):
if (not hasattr(rdmt, 'ComputePrincipalAxesAndMomentsFromGyrationMatrix')):
return
molBlock = '''\
RDKit 3D
4 3 0 0 0 0 0 0 0 0999 V2000
-0.1888 1.3224 -0.2048 F 0 0 0 0 0 0 0 0 0 0 0 0
-0.0790 0.1671 0.6070 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.3083 -0.8939 -0.2236 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1.5761 -0.5956 -0.1786 Br 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 6
2 3 1 0
2 4 1 0
M END
'''
axesRef = (
(-0.0009, -0.0246, 0.9997),
(-0.0559, -0.9981, -0.0246),
( 0.9984, -0.0559, -0.0004)
)
momentsRef = ( 0.1212, 0.7343, 1.0596)
m = Chem.MolFromMolBlock(molBlock)
axes, moments = rdmt.ComputePrincipalAxesAndMomentsFromGyrationMatrix(m.GetConformer())
self.assertIsNotNone(axes)
self.assertIsNotNone(moments)
for y in range(3):
for x in range(3):
self.assertAlmostEqual(axes[y][x], axesRef[y][x], 3)
self.assertAlmostEqual(moments[y], momentsRef[y], 3)
failed = False
try:
axes, moments = rdmt.ComputePrincipalAxesAndMomentsFromGyrationMatrix(m.GetConformer(), weights = (0.5, 0.5))
except:
failed = True
self.assertTrue(failed)
axesWeightedRef = (
( 0.0189, -0.0114, 0.9998),
(-0.2245, 0.9744, 0.0153),
( 0.9743, 0.2247, -0.0158)
)
momentsWeightedRef = ( 0.0847, 0.4649, 1.4712)
axesWeighted, momentsWeighted = rdmt.ComputePrincipalAxesAndMomentsFromGyrationMatrix(
m.GetConformer(), weights = (0.1, 0.2, 0.3, 0.4))
self.assertIsNotNone(axesWeighted)
self.assertIsNotNone(momentsWeighted)
for y in range(3):
for x in range(3):
self.assertAlmostEqual(abs(axesWeighted[y][x]), abs(axesWeightedRef[y][x]), 3)
self.assertAlmostEqual(abs(momentsWeighted[y]), abs(momentsWeightedRef[y]), 3)
def testGetSetBondLength(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
'3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
dist = rdmt.GetBondLength(conf, 0, 19)
self.failUnlessAlmostEqual(dist, 1.36, 2)
rdmt.SetBondLength(conf, 0, 19, 2.5)
dist = rdmt.GetBondLength(conf, 0, 19)
self.failUnlessAlmostEqual(dist, 2.5, 1)
rdmt.SetBondLength(conf, 19, 0, 3.0)
dist = rdmt.GetBondLength(conf, 0, 19)
self.failUnlessAlmostEqual(dist, 3.0, 1)
def testGetSetAngle(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
'3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, 109.7, 1)
rdmt.SetAngleDeg(conf, 0, 19, 21, 125.0)
angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, 125.0, 1)
rdmt.SetAngleRad(conf, 21, 19, 0, math.pi / 2.)
angle = rdmt.GetAngleRad(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, math.pi / 2., 1)
angle = rdmt.GetAngleDeg(conf, 0, 19, 21)
self.failUnlessAlmostEqual(angle, 90.0, 1)
def testGetSetDihedral(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
'3-cyclohexylpyridine.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
dihedral = rdmt.GetDihedralDeg(conf, 0, 19, 21, 24)
self.failUnlessAlmostEqual(dihedral, 176.05, 2)
rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, 65.0)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, 65.0, 1)
rdmt.SetDihedralDeg(conf, 8, 0, 19, 21, -130.0)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -130.0, 1)
rdmt.SetDihedralRad(conf, 21, 19, 0, 8, -2. / 3. * math.pi)
dihedral = rdmt.GetDihedralRad(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -2. / 3. * math.pi, 1)
dihedral = rdmt.GetDihedralDeg(conf, 8, 0, 19, 21)
self.failUnlessAlmostEqual(dihedral, -120.0, 1)
def testGetSetDihedralThroughTripleBond(self):
file = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolTransforms', 'test_data',
'github1262_2.mol')
m = Chem.MolFromMolFile(file, True, False)
conf = m.GetConformer()
rdmt.SetDihedralDeg(conf, 6, 1, 2, 9, 0.0)
dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9)
self.failUnlessAlmostEqual(dihedral, 0.0, 1)
dist = rdmt.GetBondLength(conf, 6, 9)
rdmt.SetDihedralDeg(conf, 6, 1, 2, 9, 120.0)
dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9)
self.failUnlessAlmostEqual(dihedral, 120.0, 1)
dist2 = rdmt.GetBondLength(conf, 6, 7)
self.failUnlessAlmostEqual(dist, dist2, 1)
rdmt.SetDihedralDeg(conf, 6, 1, 2, 9, 180.0)
dihedral = rdmt.GetDihedralDeg(conf, 6, 1, 2, 9)
self.failUnlessAlmostEqual(dihedral, 180.0, 1)
dist3 = rdmt.GetBondLength(conf, 6, 9)
self.failIfAlmostEqual(dist, dist3, 1)
exceptionRaised = False
try:
rdmt.SetDihedralDeg(conf, 6, 0, 3, 9, 0.0)
except ValueError:
exceptionRaised = True
self.failUnless(exceptionRaised)
if __name__ == "__main__":
unittest.main()
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