def testGithub1761(self):
mol = Chem.MolFromSmiles('CC(F)(Cl)C(F)(Cl)C')
self.assertRaises(OverflowError,
lambda: rdMD.GetMorganFingerprint(mol, -1))
self.assertRaises(OverflowError,
lambda: rdMD.GetHashedMorganFingerprint(mol, 0, -1))
self.assertRaises(ValueError,
lambda: rdMD.GetHashedMorganFingerprint(mol, 0, 0))
def calculateMol(self, m, smiles, internalParsing=False):
counts = list(
rd.GetHashedMorganFingerprint(m,
radius=self.radius,
nBits=self.nbits))
counts = [clip(x, smiles) for x in counts]
return counts
def featurize(self, x):
if self.input_type == 'smiles':
x_ = x
x = Chem.MolFromSmiles(x)
if x is None:
raise ValueError('cannot convert Mol from SMILES %s' % x_)
if self.input_type == 'any':
if not isinstance(x, Chem.rdchem.Mol):
x_ = x
x = Chem.MolFromSmiles(x)
if x is None:
raise ValueError('cannot convert Mol from SMILES %s' % x_)
if self.counting:
return count_fp(rdMol.GetHashedMorganFingerprint(x, radius=self.radius,
nBits=self.n_bits), dim=self.n_bits)
else:
return list(rdMol.GetMorganFingerprintAsBitVect(x, radius=self.radius, nBits=self.n_bits))
def testMorganFingerprints(self):
mol = Chem.MolFromSmiles('CC(F)(Cl)C(F)(Cl)C')
fp = rdMD.GetMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
mol = Chem.MolFromSmiles('CC')
fp = rdMD.GetMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 1)
self.assertTrue(list(fp.GetNonzeroElements().values())[0] == 2)
fp = rdMD.GetMorganFingerprint(mol, 0, useCounts=False)
self.assertTrue(len(fp.GetNonzeroElements()) == 1)
self.assertTrue(list(fp.GetNonzeroElements().values())[0] == 1)
mol = Chem.MolFromSmiles('CC(F)(Cl)C(F)(Cl)C')
fp = rdMD.GetHashedMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
fp = rdMD.GetMorganFingerprint(mol, 1)
self.assertTrue(len(fp.GetNonzeroElements()) == 8)
fp = rdMD.GetHashedMorganFingerprint(mol, 1)
self.assertTrue(len(fp.GetNonzeroElements()) == 8)
fp = rdMD.GetMorganFingerprint(mol, 2)
self.assertTrue(len(fp.GetNonzeroElements()) == 9)
mol = Chem.MolFromSmiles('CC(F)(Cl)[C@](F)(Cl)C')
fp = rdMD.GetMorganFingerprint(mol, 0)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
fp = rdMD.GetMorganFingerprint(mol, 1)
self.assertTrue(len(fp.GetNonzeroElements()) == 8)
fp = rdMD.GetMorganFingerprint(mol, 2)
self.assertTrue(len(fp.GetNonzeroElements()) == 9)
fp = rdMD.GetMorganFingerprint(mol, 0, useChirality=True)
self.assertTrue(len(fp.GetNonzeroElements()) == 4)
fp = rdMD.GetMorganFingerprint(mol, 1, useChirality=True)
self.assertTrue(len(fp.GetNonzeroElements()) == 9)
fp = rdMD.GetMorganFingerprint(mol, 2, useChirality=True)
self.assertTrue(len(fp.GetNonzeroElements()) == 10)
mol = Chem.MolFromSmiles('CCCCC')
fp = rdMD.GetMorganFingerprint(mol, 0, fromAtoms=(0, ))
self.assertTrue(len(fp.GetNonzeroElements()) == 1)
mol = Chem.MolFromSmiles('CC1CC1')
vs1 = rdMD.GetConnectivityInvariants(mol)
self.assertEqual(len(vs1), mol.GetNumAtoms())
fp1 = rdMD.GetMorganFingerprint(mol, 2, invariants=vs1)
fp2 = rdMD.GetMorganFingerprint(mol, 2)
self.assertEqual(fp1, fp2)
vs2 = rdMD.GetConnectivityInvariants(mol, False)
self.assertEqual(len(vs2), mol.GetNumAtoms())
self.assertNotEqual(vs1, vs2)
fp1 = rdMD.GetMorganFingerprint(mol, 2, invariants=vs2)
self.assertNotEqual(fp1, fp2)
mol = Chem.MolFromSmiles('Cc1ccccc1')
vs1 = rdMD.GetFeatureInvariants(mol)
self.assertEqual(len(vs1), mol.GetNumAtoms())
self.assertEqual(vs1[0], 0)
self.assertNotEqual(vs1[1], 0)
self.assertEqual(vs1[1], vs1[2])
self.assertEqual(vs1[1], vs1[3])
self.assertEqual(vs1[1], vs1[4])
mol = Chem.MolFromSmiles('FCCCl')
vs1 = rdMD.GetFeatureInvariants(mol)
self.assertEqual(len(vs1), mol.GetNumAtoms())
self.assertEqual(vs1[1], 0)
self.assertEqual(vs1[2], 0)
self.assertNotEqual(vs1[0], 0)
self.assertEqual(vs1[0], vs1[3])
fp1 = rdMD.GetMorganFingerprint(mol, 0, invariants=vs1)
fp2 = rdMD.GetMorganFingerprint(mol, 0, useFeatures=True)
self.assertEqual(fp1, fp2)
def calculateMol(self, m, smiles, internalParsing=False):
v = rd.GetHashedMorganFingerprint(m,
radius=self.radius, nBits=self.nbits)
return clip_sparse(v, self.nbits)
def calculateMol(self, m, smiles, internalParsing=False):
return clip_sparse(rd.GetHashedMorganFingerprint(
m, radius=self.radius, nBits=self.nbits, invariants=rd.GetFeatureInvariants(m)),
self.nbits)
def calculateMol(self, m, smiles, internalParsing=False):
return clip_sparse(rd.GetHashedMorganFingerprint(
m, radius=self.radius, nBits=self.nbits, useChirality=True),
self.nbits)
