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https://github.com/rdkit/rdkit.git
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bb066c43f4
* fix aliasing bug in MultithreadedSDMolSupplier * update GeneralFileReader to v2 API * add backwards incompatibility note * v1 of this * The helper function needs to be inline * forgot the tests * allow non-threadsafe builds * MultithreadedMolSuppliers can now be destroyed without being used. This was previously not possible * add callbacks to the multithreaded readers * document the new functions * switch to storing the queues in unique_ptrs * does not work * only do those tests when in MT mode * more generalfilereader cleanup * tests pass * passes tests * extremely basic python wrapper * better wrapper * does not work * tests pass * test data * fix failing test on ARM macs we need to followup on why the wedging is different here * move some stuff to the cpp file the idea is to have the windows DLL builds not break * fix(?) win64 linkage problems * remove a warning in non-multi-threaded builds * fix non-multi-threaded work * well, at least local windows builds work * remove duplicated code * refactoring simplification? * simplify mutext handling * review suggestions
57 lines
2.0 KiB
Python
57 lines
2.0 KiB
Python
#
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# Copyright (C) 2024 Greg Landrum and other RDKit contributors
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# @@ All Rights Reserved @@
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#
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# This file is part of the RDKit.
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# The contents are covered by the terms of the BSD license
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# which is included in the file license.txt, found at the root
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# of the RDKit source tree.
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import unittest
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#
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from rdkit import Chem
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from rdkit.Chem import rdMolProcessing
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from rdkit.Chem import rdFingerprintGenerator
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from rdkit import DataStructs
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from rdkit import RDConfig
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class TestCase(unittest.TestCase):
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def setUp(self):
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self.smiFile = RDConfig.RDBaseDir + '/Regress/Data/zinc.leads.500.q.smi'
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self.sdFile = RDConfig.RDBaseDir + "/Data/NCI/first_200.props.sdf"
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def test1(self):
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fpg = rdFingerprintGenerator.GetMorganGenerator()
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fps = rdMolProcessing.GetFingerprintsForMolsInFile(self.smiFile)
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self.assertEqual(len(fps), 499)
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with Chem.SmilesMolSupplier(self.smiFile, delimiter='\t') as suppl:
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mols = [next(suppl) for _ in range(3)]
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nfps = [fpg.GetFingerprint(m) for m in mols]
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self.assertEqual(DataStructs.TanimotoSimilarity(fps[0], fps[1]),
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DataStructs.TanimotoSimilarity(nfps[0], nfps[1]))
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fps = rdMolProcessing.GetFingerprintsForMolsInFile(self.sdFile)
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self.assertEqual(len(fps), 200)
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with Chem.SDMolSupplier(self.sdFile) as suppl:
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mols = [next(suppl) for _ in range(3)]
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nfps = [fpg.GetFingerprint(m) for m in mols]
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self.assertAlmostEqual(DataStructs.TanimotoSimilarity(fps[0], fps[1]), 0.0638, places=3)
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def test2(self):
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fpg = rdFingerprintGenerator.GetMorganGenerator(radius=2)
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fps = rdMolProcessing.GetFingerprintsForMolsInFile(self.smiFile, generator=fpg)
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self.assertEqual(len(fps), 499)
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with Chem.SmilesMolSupplier(self.smiFile, delimiter='\t') as suppl:
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mols = [next(suppl) for _ in range(3)]
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nfps = [fpg.GetFingerprint(m) for m in mols]
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self.assertEqual(DataStructs.TanimotoSimilarity(fps[0], fps[1]),
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DataStructs.TanimotoSimilarity(nfps[0], nfps[1]))
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if __name__ == '__main__': # pragma: nocover
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unittest.main()
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