def testAtomPairTypes(self):
params = rdMD.AtomPairsParameters
mol = Chem.MolFromSmiles("C=C")
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))==\
rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1)))
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))==\
1 | (1 | 1<<params.numPiBits)<<params.numBranchBits)
mol = Chem.MolFromSmiles("C#CO")
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))!=\
rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1)))
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))==\
1 | (2 | 1<<params.numPiBits)<<params.numBranchBits)
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1))==\
2 | (2 | 1<<params.numPiBits)<<params.numBranchBits)
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(2))==\
1 | (0 | 3<<params.numPiBits)<<params.numBranchBits)
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1),1)==\
1 | (2 | 1<<params.numPiBits)<<params.numBranchBits)
self.assertTrue(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1),2)==\
0 | (2 | 1<<params.numPiBits)<<params.numBranchBits)
def testAtomPairTypesChirality(self):
mols = [
Chem.MolFromSmiles(x)
for x in ("CC(F)Cl", "C[C@@H](F)Cl", "C[C@H](F)Cl")
]
self.assertEqual(rdMD.GetAtomPairAtomCode(mols[0].GetAtomWithIdx(1)),
rdMD.GetAtomPairAtomCode(mols[1].GetAtomWithIdx(1)))
self.assertEqual(rdMD.GetAtomPairAtomCode(mols[0].GetAtomWithIdx(1)),
rdMD.GetAtomPairAtomCode(mols[2].GetAtomWithIdx(1)))
self.assertEqual(
rdMD.GetAtomPairAtomCode(mols[0].GetAtomWithIdx(1),
includeChirality=True),
rdMD.GetAtomPairAtomCode(mols[0].GetAtomWithIdx(1)))
self.assertNotEqual(
rdMD.GetAtomPairAtomCode(mols[0].GetAtomWithIdx(1),
includeChirality=True),
rdMD.GetAtomPairAtomCode(mols[1].GetAtomWithIdx(1),
includeChirality=True))
self.assertNotEqual(
rdMD.GetAtomPairAtomCode(mols[0].GetAtomWithIdx(1),
includeChirality=True),
rdMD.GetAtomPairAtomCode(mols[2].GetAtomWithIdx(1),
includeChirality=True))
self.assertNotEqual(
rdMD.GetAtomPairAtomCode(mols[1].GetAtomWithIdx(1),
includeChirality=True),
rdMD.GetAtomPairAtomCode(mols[2].GetAtomWithIdx(1),
includeChirality=True))
fps = [rdMD.GetAtomPairFingerprint(x) for x in mols]
chiralFps = [
rdMD.GetAtomPairFingerprint(x, includeChirality=True) for x in mols
]
for mol, fp, cfp in zip(mols, fps, chiralFps):
ac0 = rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))
ac1 = rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1))
self.assertTrue(
rdMD.GetAtomPairCode(ac0, ac1, 1) in fp.GetNonzeroElements())
ac0 = rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0),
includeChirality=True)
ac1 = rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1),
includeChirality=True)
self.assertFalse(
rdMD.GetAtomPairCode(ac0, ac1, 1, includeChirality=True) in
fp.GetNonzeroElements())
self.assertTrue(
rdMD.GetAtomPairCode(ac0, ac1, 1, includeChirality=True) in
cfp.GetNonzeroElements())
