def testUSR(self):
mol = Chem.MolFromSmiles("CC")
AllChem.Compute2DCoords(mol)
self.failUnlessRaises(ValueError, lambda: rdMD.GetUSR(mol))
mol = Chem.MolFromSmiles("C1CCCCC1")
mol = Chem.AddHs(mol)
self.failUnlessRaises(ValueError, lambda: rdMD.GetUSR(mol))
AllChem.Compute2DCoords(mol)
usr = rdMD.GetUSR(mol)
self.failUnlessEqual(len(usr), 12)
self.failUnlessRaises(ValueError, lambda: rdMD.GetUSRDistributions([]))
conf = mol.GetConformer()
coords = [conf.GetAtomPosition(i) for i in range(mol.GetNumAtoms())]
dist = rdMD.GetUSRDistributions(coords)
self.failUnlessEqual(len(dist), 4)
self.failUnlessEqual(len(dist[0]), mol.GetNumAtoms())
self.failUnlessRaises(ValueError,
lambda: rdMD.GetUSRFromDistributions([]))
usr2 = rdMD.GetUSRFromDistributions(dist)
self.failUnlessEqual(usr, usr2)
self.failUnlessRaises(
ValueError, lambda: rdMD.GetUSRDistributionsFromPoints(coords, []))
p = []
dist = rdMD.GetUSRDistributions(coords, p)
self.failUnlessRaises(
ValueError, lambda: rdMD.GetUSRDistributionsFromPoints([], p))
dist2 = rdMD.GetUSRDistributionsFromPoints(coords, p)
usr2 = rdMD.GetUSRFromDistributions(dist2)
self.failUnlessEqual(usr, usr2)
mol2 = Chem.MolFromSmiles("C1CCCCC1")
mol2 = Chem.AddHs(mol2)
AllChem.Compute2DCoords(mol2)
usr2 = rdMD.GetUSR(mol2)
self.failUnlessRaises(ValueError,
lambda: rdMD.GetUSRScore(usr, usr2[:2]))
self.failUnlessEqual(rdMD.GetUSRScore(usr, usr2), 1.0)
m1 = [
4.44, 2.98, 1.04, 4.55, 4.70, 0.23, 8.30, 16.69, -22.97, 7.37,
15.64, 0.51
]
m2 = [
4.39, 3.11, 1.36, 4.50, 4.44, 0.09, 8.34, 16.78, -23.20, 7.15,
16.52, 0.13
]
self.failUnlessAlmostEqual(rdMD.GetUSRScore(m1, m2), 0.812, 2)
def testUSRCAT(self):
mol = Chem.MolFromSmiles("CC")
AllChem.Compute2DCoords(mol)
self.assertRaises(ValueError, lambda: rdMD.GetUSRCAT(mol))
mol = Chem.MolFromSmiles("C1CCCCC1")
mol = Chem.AddHs(mol)
self.assertRaises(ValueError, lambda: rdMD.GetUSRCAT(mol))
AllChem.Compute2DCoords(mol)
usr = rdMD.GetUSRCAT(mol)
self.assertEqual(len(usr), 60)
self.assertRaises(ValueError, lambda: rdMD.GetUSRCAT(mol, atomSelections=[]))
atoms = [[1, 2, 3, 4, 5, 6], []]
usr2 = rdMD.GetUSRCAT(mol, atomSelections=atoms)
self.assertEqual(len(usr2), 36)
atoms = [[1, 2, 3, 4, 5, 6], [], [], []]
usr2 = rdMD.GetUSRCAT(mol, atomSelections=atoms)
self.assertEqual(len(usr2), 60)
self.assertEqual(rdMD.GetUSRScore(usr, usr2, weights=[1.0, 1.0, 1.0, 1.0, 1.0]), 1.0)
