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from rdkit import Chem
from rdkit.Chem import rdFingerprintGenerator
import unittest
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testAtomPairGenerator(self):
m = Chem.MolFromSmiles('CCC')
g = rdFingerprintGenerator.GetAtomPairGenerator()
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 2)
fp = g.GetCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 2)
fp = g.GetSparseFingerprint(m)
nzc = fp.GetNumOnBits()
self.assertEqual(nzc, 3)
fp = g.GetFingerprint(m)
nzc = fp.GetNumOnBits()
self.assertEqual(nzc, 3)
g = rdFingerprintGenerator.GetAtomPairGenerator(
atomInvariantsGenerator=rdFingerprintGenerator.GetAtomPairAtomInvGen())
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 2)
g = rdFingerprintGenerator.GetAtomPairGenerator(minDistance=2)
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 1)
g = rdFingerprintGenerator.GetAtomPairGenerator(maxDistance=1)
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 1)
g = rdFingerprintGenerator.GetAtomPairGenerator(useCountSimulation=False)
fp = g.GetSparseFingerprint(m)
nzc = fp.GetNumOnBits()
self.assertEqual(nzc, 2)
invGen = rdFingerprintGenerator.GetAtomPairAtomInvGen(includeChirality=False)
invGenChirality = rdFingerprintGenerator.GetAtomPairAtomInvGen(includeChirality=True)
g = rdFingerprintGenerator.GetAtomPairGenerator(includeChirality=False,
atomInvariantsGenerator=invGen)
gChirality = rdFingerprintGenerator.GetAtomPairGenerator(
includeChirality=True, atomInvariantsGenerator=invGenChirality)
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
fpChirality = gChirality.GetSparseCountFingerprint(m)
nzChirality = fpChirality.GetNonzeroElements()
self.assertNotEqual(nz.keys(), nzChirality.keys())
def testMorganGenerator(self):
m = Chem.MolFromSmiles('CCCC(=O)O')
g = rdFingerprintGenerator.GetMorganGenerator(3)
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 14)
invgen = rdFingerprintGenerator.GetMorganAtomInvGen()
g = rdFingerprintGenerator.GetMorganGenerator(radius=3, atomInvariantsGenerator=invgen)
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 14)
invgen = rdFingerprintGenerator.GetMorganFeatureAtomInvGen()
g = rdFingerprintGenerator.GetMorganGenerator(radius=3, atomInvariantsGenerator=invgen)
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 13)
ms = [Chem.MolFromSmiles(x, sanitize=False) for x in ('C1=CC=CN=N1', 'C1C=CC=NN=1')]
for m in ms:
m.UpdatePropertyCache()
Chem.GetSymmSSSR(m)
g = rdFingerprintGenerator.GetMorganGenerator(radius=2, useBondTypes=True)
self.assertNotEqual(g.GetSparseCountFingerprint(ms[0]), g.GetSparseCountFingerprint(ms[1]))
g = rdFingerprintGenerator.GetMorganGenerator(radius=2, useBondTypes=False)
self.assertEqual(g.GetSparseCountFingerprint(ms[0]), g.GetSparseCountFingerprint(ms[1]))
binvgen = rdFingerprintGenerator.GetMorganBondInvGen(useBondTypes=False)
g2 = rdFingerprintGenerator.GetMorganGenerator(radius=2, bondInvariantsGenerator=binvgen)
self.assertEqual(g.GetSparseCountFingerprint(ms[0]), g2.GetSparseCountFingerprint(ms[0]))
self.assertEqual(g.GetSparseCountFingerprint(ms[1]), g2.GetSparseCountFingerprint(ms[1]))
def testRDKitFPGenerator(self):
m = Chem.MolFromSmiles('CCCCC')
g = rdFingerprintGenerator.GetRDKitFPGenerator()
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 8)
def testTopologicalTorsionGenerator(self):
m = Chem.MolFromSmiles('CCCCC')
g = rdFingerprintGenerator.GetTopologicalTorsionGenerator()
fp = g.GetSparseCountFingerprint(m)
nz = fp.GetNonzeroElements()
self.assertEqual(len(nz), 1)
def testBulk(self):
m1 = Chem.MolFromSmiles('CCC')
m2 = Chem.MolFromSmiles('OCCCCC')
m3 = Chem.MolFromSmiles('CCCCC')
g = rdFingerprintGenerator.GetAtomPairGenerator()
results = rdFingerprintGenerator.GetSparseCountFPs([m1, m2, m3],
rdFingerprintGenerator.AtomPairFP)
self.assertEqual(results[0], g.GetSparseCountFingerprint(m1))
self.assertEqual(results[1], g.GetSparseCountFingerprint(m2))
self.assertEqual(results[2], g.GetSparseCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetMorganGenerator(2)
results = rdFingerprintGenerator.GetSparseCountFPs([m1, m2, m3],
rdFingerprintGenerator.MorganFP)
self.assertEqual(results[0], g.GetSparseCountFingerprint(m1))
self.assertEqual(results[1], g.GetSparseCountFingerprint(m2))
self.assertEqual(results[2], g.GetSparseCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetRDKitFPGenerator()
results = rdFingerprintGenerator.GetSparseCountFPs([m1, m2, m3], rdFingerprintGenerator.RDKitFP)
self.assertEqual(results[0], g.GetSparseCountFingerprint(m1))
self.assertEqual(results[1], g.GetSparseCountFingerprint(m2))
self.assertEqual(results[2], g.GetSparseCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetTopologicalTorsionGenerator()
results = rdFingerprintGenerator.GetSparseCountFPs([m1, m2, m3],
rdFingerprintGenerator.TopologicalTorsionFP)
self.assertEqual(results[0], g.GetSparseCountFingerprint(m1))
self.assertEqual(results[1], g.GetSparseCountFingerprint(m2))
self.assertEqual(results[2], g.GetSparseCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetAtomPairGenerator()
results = rdFingerprintGenerator.GetSparseFPs([m1, m2, m3], rdFingerprintGenerator.AtomPairFP)
self.assertEqual(results[0], g.GetSparseFingerprint(m1))
self.assertEqual(results[1], g.GetSparseFingerprint(m2))
self.assertEqual(results[2], g.GetSparseFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetMorganGenerator(2)
results = rdFingerprintGenerator.GetSparseFPs([m1, m2, m3], rdFingerprintGenerator.MorganFP)
self.assertEqual(results[0], g.GetSparseFingerprint(m1))
self.assertEqual(results[1], g.GetSparseFingerprint(m2))
self.assertEqual(results[2], g.GetSparseFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetRDKitFPGenerator()
results = rdFingerprintGenerator.GetSparseFPs([m1, m2, m3], rdFingerprintGenerator.RDKitFP)
self.assertEqual(results[0], g.GetSparseFingerprint(m1))
self.assertEqual(results[1], g.GetSparseFingerprint(m2))
self.assertEqual(results[2], g.GetSparseFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetTopologicalTorsionGenerator()
results = rdFingerprintGenerator.GetSparseFPs([m1, m2, m3],
rdFingerprintGenerator.TopologicalTorsionFP)
self.assertEqual(results[0], g.GetSparseFingerprint(m1))
self.assertEqual(results[1], g.GetSparseFingerprint(m2))
self.assertEqual(results[2], g.GetSparseFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetAtomPairGenerator()
results = rdFingerprintGenerator.GetCountFPs([m1, m2, m3], rdFingerprintGenerator.AtomPairFP)
self.assertEqual(results[0], g.GetCountFingerprint(m1))
self.assertEqual(results[1], g.GetCountFingerprint(m2))
self.assertEqual(results[2], g.GetCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetMorganGenerator(2)
results = rdFingerprintGenerator.GetCountFPs([m1, m2, m3], rdFingerprintGenerator.MorganFP)
self.assertEqual(results[0], g.GetCountFingerprint(m1))
self.assertEqual(results[1], g.GetCountFingerprint(m2))
self.assertEqual(results[2], g.GetCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetRDKitFPGenerator()
results = rdFingerprintGenerator.GetCountFPs([m1, m2, m3], rdFingerprintGenerator.RDKitFP)
self.assertEqual(results[0], g.GetCountFingerprint(m1))
self.assertEqual(results[1], g.GetCountFingerprint(m2))
self.assertEqual(results[2], g.GetCountFingerprint(m3))
self.assertEqual(len(results), 3)
g = rdFingerprintGenerator.GetTopologicalTorsionGenerator()
results = rdFingerprintGenerator.GetCountFPs([m1, m2, m3],
rdFingerprintGenerator.TopologicalTorsionFP)
self.assertEqual(results[0], g.GetCountFingerprint(m1))
self.assertEqual(results[1], g.GetCountFingerprint(m2))
self.assertEqual(results[2], g.GetCountFingerprint(m3))
self.assertEqual(len(results), 3)
def testNumBitsPerFeature(self):
m1 = Chem.MolFromSmiles('CCCO')
g = rdFingerprintGenerator.GetRDKitFPGenerator(minPath=1, maxPath=2)
fp = g.GetFingerprint(m1)
self.assertEqual(fp.GetNumOnBits(), 8)
g = rdFingerprintGenerator.GetRDKitFPGenerator(minPath=1, maxPath=2, numBitsPerFeature=1)
fp = g.GetFingerprint(m1)
self.assertEqual(fp.GetNumOnBits(), 4)
if __name__ == '__main__':
unittest.main()
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