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#
# Copyright (C) 2024 Greg Landrum and other RDKit contributors
# @@ All Rights Reserved @@
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
import unittest
#
from rdkit import Chem
from rdkit.Chem import rdMolProcessing
from rdkit.Chem import rdFingerprintGenerator
from rdkit import DataStructs
from rdkit import RDConfig
class TestCase(unittest.TestCase):
def setUp(self):
self.smiFile = RDConfig.RDBaseDir + '/Regress/Data/zinc.leads.500.q.smi'
self.sdFile = RDConfig.RDBaseDir + "/Data/NCI/first_200.props.sdf"
def test1(self):
fpg = rdFingerprintGenerator.GetMorganGenerator()
fps = rdMolProcessing.GetFingerprintsForMolsInFile(self.smiFile)
self.assertEqual(len(fps), 499)
with Chem.SmilesMolSupplier(self.smiFile, delimiter='\t') as suppl:
mols = [next(suppl) for _ in range(3)]
nfps = [fpg.GetFingerprint(m) for m in mols]
self.assertEqual(DataStructs.TanimotoSimilarity(fps[0], fps[1]),
DataStructs.TanimotoSimilarity(nfps[0], nfps[1]))
fps = rdMolProcessing.GetFingerprintsForMolsInFile(self.sdFile)
self.assertEqual(len(fps), 200)
with Chem.SDMolSupplier(self.sdFile) as suppl:
mols = [next(suppl) for _ in range(3)]
nfps = [fpg.GetFingerprint(m) for m in mols]
self.assertAlmostEqual(DataStructs.TanimotoSimilarity(fps[0], fps[1]), 0.0638, places=3)
def test2(self):
fpg = rdFingerprintGenerator.GetMorganGenerator(radius=2)
fps = rdMolProcessing.GetFingerprintsForMolsInFile(self.smiFile, generator=fpg)
self.assertEqual(len(fps), 499)
with Chem.SmilesMolSupplier(self.smiFile, delimiter='\t') as suppl:
mols = [next(suppl) for _ in range(3)]
nfps = [fpg.GetFingerprint(m) for m in mols]
self.assertEqual(DataStructs.TanimotoSimilarity(fps[0], fps[1]),
DataStructs.TanimotoSimilarity(nfps[0], nfps[1]))
if __name__ == '__main__': # pragma: nocover
unittest.main()
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