def testProvidingCPCI(self):
"""
test for a ring molecule, repeated generating a conformer with and without enforcing
an additional +ve interaction between a pair of non-bonded atoms (termed CPCI,
custom pairwise charge-like interaciton), in every iteration, applying CPCI should
yield a conformer where this pair of atoms are further apart.
"""
for i in range(5):
ps = rdDistGeom.EmbedParameters()
ps.randomSeed = i
ps.useBasicKnowledge = True
ps.useRandomCoords = False
m1 = Chem.MolFromSmiles("C1CCCC1C")
self.assertEqual(rdDistGeom.EmbedMolecule(m1, ps), 0)
m2 = Chem.MolFromSmiles("C1CCCC1C")
ps = rdDistGeom.EmbedParameters()
ps.randomSeed = i
ps.useRandomCoords = False
ps.useBasicKnowledge = True
ps.SetCPCI({(0, 3): 0.9})
self.assertEqual(rdDistGeom.EmbedMolecule(m2, ps), 0)
conf1 = m1.GetConformer()
conf2 = m2.GetConformer()
self.assertTrue(
(conf2.GetAtomPosition(3) -
conf2.GetAtomPosition(0)).Length() >
(conf1.GetAtomPosition(3) - conf1.GetAtomPosition(0)).Length())
def testScaleBoundsMatForce(self):
"""
for pentane, set a target distance for the 1-5 distance, and generate conformers with changing weights for (all) the atom pair distance restraints,
the conformer with the stronger weight for the atom pairs will always have a 1-5 distance closer to the target value than that with the weaker weight.
"""
target = 4
for i in range(5):
ps = rdDistGeom.EmbedParameters()
ps.randomSeed = i
ps.useBasicKnowledge = True
ps.useRandomCoords = False
m1 = Chem.MolFromSmiles("CCCCC")
bm1 = rdDistGeom.GetMoleculeBoundsMatrix(m1)
bm1[0,4] = target
bm1[4,0] = target
DG.DoTriangleSmoothing(bm1)
ps.boundsMatForceScaling = 0.1
ps.SetBoundsMat(bm1)
self.assertEqual(rdDistGeom.EmbedMolecule(m1,ps),0)
m2 = Chem.MolFromSmiles("CCCCC")
ps = rdDistGeom.EmbedParameters()
ps.randomSeed = i
ps.useBasicKnowledge = True
ps.useRandomCoords = False
ps.boundsMatForceScaling = 10
ps.SetBoundsMat(bm1)
self.assertEqual(rdDistGeom.EmbedMolecule(m2,ps),0)
conf1 = m1.GetConformer()
conf2 = m2.GetConformer()
self.assertTrue(abs((conf2.GetAtomPosition(4)-conf2.GetAtomPosition(0)).Length() - target) < abs((conf1.GetAtomPosition(4)-conf1.GetAtomPosition(0)).Length() - target))
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 testProvidingBoundsMatrix(self):
m1 = Chem.MolFromSmiles("C1CCC1C")
bm1 = rdDistGeom.GetMoleculeBoundsMatrix(m1)
bm1[0, 3] = 1.21
bm1[3, 0] = 1.20
bm1[2, 3] = 1.21
bm1[3, 2] = 1.20
bm1[4, 3] = 1.21
bm1[3, 4] = 1.20
DG.DoTriangleSmoothing(bm1)
ps = rdDistGeom.EmbedParameters()
ps.useRandomCoords = True
ps.SetBoundsMat(bm1)
ps.randomSeed = 0xf00d
self.assertEqual(rdDistGeom.EmbedMolecule(m1, ps), 0)
conf = m1.GetConformer()
self.assertAlmostEqual(
(conf.GetAtomPosition(3) - conf.GetAtomPosition(0)).Length(),
1.2,
delta=0.05)
self.assertAlmostEqual(
(conf.GetAtomPosition(3) - conf.GetAtomPosition(2)).Length(),
1.2,
delta=0.05)
self.assertAlmostEqual(
(conf.GetAtomPosition(3) - conf.GetAtomPosition(4)).Length(),
1.2,
delta=0.05)
def embed_bounds_matrix(mol: Mol,
bounds_matrix: np.ndarray,
seed: int = 42) -> int:
DistanceGeometry.DoTriangleSmoothing(bounds_matrix)
ps = rdDistGeom.EmbedParameters()
ps.numThreads = 0 # max number of threads supported by the system will be used
ps.useRandomCoords = True # recommended for larger molecules
ps.clearConfs = False
ps.randomSeed = seed
ps.SetBoundsMat(bounds_matrix)
return rdDistGeom.EmbedMolecule(mol, ps)
#print("({}, {}) {} < x < {}".format(i, j, bm[j, i], bm[i, j]))
if bm[i, j] < bm[j, i]:
print(
" ***** Assertion failed !! (Before smoothing) *****"
)
assert (bm[i, j] >= bm[j, i])
if DG.DoTriangleSmoothing(bm) == False:
print("Smoothing failed")
for i in range(len(bm)):
for j in range(i + 1, len(bm)):
#print("({}, {}) {} < x < {}".format(i, j, bm[j, i], bm[i, j]))
if bm[i, j] < bm[j, i]:
print(
" ***** Assertion failed !! (After smoothing) *****")
assert (bm[i, j] >= bm[j, i])
ps = rdDistGeom.EmbedParameters()
ps.useRandomCoords = True
ps.SetBoundsMat(bm)
ps.randomSeed = 0xf00d
try:
rdDistGeom.EmbedMolecule(mol, ps)
except:
print("Failed to generate coordinates")
ps = rdDistGeom.ETKDG()
ps.useRandomCoords = True
ps.randomSeed = 0xf00d
rdDistGeom.EmbedMolecule(mol, ps)
w.write(mol)
