mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-06 22:39:55 +08:00
a06c921a79
* for-loop modernization * declaration and initialization together * switch statements, min&max from std * switch statement * use of std min&max * fixed unsigned int to int comparison * implement switch statement * fix unsigned int to int comparison * revert previous mistake * Update Code/DataStructs/DiscreteValueVect.cpp Co-authored-by: Greg Landrum <greg.landrum@gmail.com> * implemented suggestions --------- Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
326 lines
8.8 KiB
Python
Executable File
326 lines
8.8 KiB
Python
Executable File
import pickle
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import random
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import unittest
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import numpy
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from rdkit import DataStructs, RDConfig
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def feq(a, b, tol=1e-4):
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return abs(a - b) < tol
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def test0FromList(self):
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bv1 = DataStructs.SparseBitVect(1000)
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bv2 = DataStructs.SparseBitVect(1000)
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obits = range(0, 1000, 3)
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for bit in obits:
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bv1.SetBit(bit)
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bv2.SetBitsFromList(obits)
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for i in range(1000):
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assert bv1.GetBit(i) == bv2.GetBit(i)
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self.assertTrue(bv1 == bv2)
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bv2.SetBit(1)
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self.assertTrue(bv1 != bv2)
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bv2.UnSetBit(1)
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self.assertTrue(bv1 == bv2)
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bv2.UnSetBitsFromList(obits)
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for i in range(1000):
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assert bv2.GetBit(i) == 0
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bv1 = DataStructs.ExplicitBitVect(1000)
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bv2 = DataStructs.ExplicitBitVect(1000)
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obits = range(0, 1000, 3)
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for bit in obits:
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bv1.SetBit(bit)
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bv2.SetBitsFromList(obits)
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for i in range(1000):
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assert bv1.GetBit(i) == bv2.GetBit(i)
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bv2.UnSetBitsFromList(obits)
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for i in range(1000):
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assert bv2.GetBit(i) == 0
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def test01BVWithAllOnes(self):
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bv1 = DataStructs.ExplicitBitVect(10, True)
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for i in range(10):
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assert bv1.GetBit(i) == 1
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def test1SparsePickle(self):
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nbits = 10000
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bv1 = DataStructs.SparseBitVect(nbits)
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for i in range(1000):
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x = random.randrange(0, nbits)
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bv1.SetBit(x)
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pkl = pickle.dumps(bv1, 1)
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bv2 = pickle.loads(pkl)
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for i in range(nbits):
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assert bv1[i] == bv2[i]
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def test2ExplicitPickle(self):
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nbits = 10000
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bv1 = DataStructs.ExplicitBitVect(nbits)
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for i in range(1000):
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x = random.randrange(0, nbits)
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bv1.SetBit(x)
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pkl = pickle.dumps(bv1, 1)
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bv2 = pickle.loads(pkl)
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for i in range(nbits):
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assert bv1[i] == bv2[i]
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def test3Bounds(self):
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nbits = 10
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bv1 = DataStructs.ExplicitBitVect(nbits)
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bv1[0]
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with self.assertRaisesRegex(IndexError, ""):
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bv1[11]
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def test4OnBitsInCommon(self):
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sz = 100
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bv1 = DataStructs.ExplicitBitVect(sz)
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bv2 = DataStructs.ExplicitBitVect(sz)
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for i in range(0, sz, 2):
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bv1.SetBit(i)
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if i < 3 * sz / 4:
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bv2.SetBit(i)
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self.assertTrue(DataStructs.AllProbeBitsMatch(bv1, bv1.ToBinary()))
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self.assertTrue(DataStructs.AllProbeBitsMatch(bv2, bv1.ToBinary()))
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self.assertFalse(DataStructs.AllProbeBitsMatch(bv1, bv2.ToBinary()))
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self.assertTrue(DataStructs.AllProbeBitsMatch(bv2, bv2.ToBinary()))
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def test5FromBitString(self):
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s1 = '1010'
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bv = DataStructs.CreateFromBitString(s1)
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self.assertTrue(len(bv) == 4)
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self.assertTrue(list(bv.GetOnBits()) == [0, 2])
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def _bulkTest(self, bvs):
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for metric in 'Tanimoto', 'Dice', 'AllBit', 'OnBit', 'RogotGoldberg':
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bulk = getattr(DataStructs, f'Bulk{metric}Similarity')
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single = getattr(DataStructs, f'{metric}Similarity')
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sims = bulk(bvs[0], bvs)
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for i, bbvs in enumerate(bvs):
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sim = single(bvs[0], bbvs)
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self.assertEqual(sim, sims[i])
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self.assertEqual(sim, single(bvs[0], bbvs.ToBinary()))
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dists = bulk(bvs[0], bvs, returnDistance=True)
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for i, bbvs in enumerate(bvs):
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dist = single(bvs[0], bbvs, returnDistance=True)
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self.assertEqual(dist, dists[i])
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self.assertEqual(dist, single(bvs[0], bbvs.ToBinary(), returnDistance=True))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
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for i, bbvs in enumerate(bvs):
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sim = DataStructs.TverskySimilarity(bvs[0], bbvs, 1, 1)
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self.assertEqual(sim, sims[i])
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sim = DataStructs.TanimotoSimilarity(bvs[0], bbvs)
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self.assertEqual(sim, sims[i])
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1, returnDistance=True)
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for i, bbvs in enumerate(bvs):
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sim = DataStructs.TverskySimilarity(bvs[0], bbvs, 1, 1, returnDistance=True)
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self.assertEqual(sim, sims[i])
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sim = DataStructs.TanimotoSimilarity(bvs[0], bbvs, returnDistance=True)
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self.assertEqual(sim, sims[i])
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def test6BulkOps(self):
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nbits = 10000
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bvs = []
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for _ in range(10):
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bv = DataStructs.ExplicitBitVect(nbits)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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bv.SetBit(x)
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bvs.append(bv)
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self._bulkTest(bvs)
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def test10BulkOps2(self):
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nbits = 10000
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bvs = []
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for _ in range(10):
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bv = DataStructs.ExplicitBitVect(nbits)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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bv.SetBit(x)
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bvs.append(bv)
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bvs = tuple(bvs)
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self._bulkTest(bvs)
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def test10BulkOps3(self):
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nbits = 10000
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bvs = numpy.empty((10, ), DataStructs.ExplicitBitVect)
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for bvi in range(10):
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bv = DataStructs.ExplicitBitVect(nbits)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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bv.SetBit(x)
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bvs[bvi] = bv
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self._bulkTest(bvs)
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def test7FPS(self):
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bv = DataStructs.ExplicitBitVect(32)
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bv.SetBit(0)
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bv.SetBit(1)
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bv.SetBit(17)
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bv.SetBit(23)
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bv.SetBit(31)
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self.assertEqual(DataStructs.BitVectToFPSText(bv), "03008280")
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bv2 = DataStructs.CreateFromFPSText("03008280")
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self.assertEqual(bv, bv2)
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self.assertRaises(ValueError, lambda: DataStructs.CreateFromFPSText("030082801"))
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bv2 = DataStructs.CreateFromFPSText("")
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self.assertEqual(bv2.GetNumBits(), 0)
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def test8BinText(self):
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bv = DataStructs.ExplicitBitVect(32)
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bv.SetBit(0)
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bv.SetBit(1)
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bv.SetBit(17)
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bv.SetBit(23)
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bv.SetBit(31)
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bv2 = DataStructs.CreateFromBinaryText(DataStructs.BitVectToBinaryText(bv))
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self.assertEqual(bv, bv2)
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bv2 = DataStructs.CreateFromBinaryText("")
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self.assertEqual(bv2.GetNumBits(), 0)
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def test9ToNumpy(self):
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import numpy
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for typ in (DataStructs.ExplicitBitVect, ):
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bv = typ(32)
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bv.SetBit(0)
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bv.SetBit(1)
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bv.SetBit(17)
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bv.SetBit(23)
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bv.SetBit(31)
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arr = numpy.zeros((32, ), 'i')
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DataStructs.ConvertToNumpyArray(bv, arr)
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for i in range(bv.GetNumBits()):
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self.assertEqual(bv[i], arr[i])
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for typ in (DataStructs.IntSparseIntVect, DataStructs.LongSparseIntVect,
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DataStructs.UIntSparseIntVect, DataStructs.ULongSparseIntVect):
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iv = typ(32)
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iv[0] = 1
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iv[1] = 1
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iv[17] = 1
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iv[23] = 1
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iv[31] = 1
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arr = numpy.zeros((32, ), 'i')
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DataStructs.ConvertToNumpyArray(iv, arr)
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for i in range(iv.GetLength()):
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self.assertEqual(iv[i], arr[i])
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def test11BulkNeighbors(self):
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nbits = 2048
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bvs = []
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for _ in range(1000):
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bv = DataStructs.ExplicitBitVect(nbits)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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bv.SetBit(x)
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bvs.append(bv)
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qs = bvs[:10]
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db = bvs[10:]
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for metric in [
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'Tanimoto', 'Cosine', 'Kulczynski', 'Dice', 'Sokal', 'McConnaughey', 'Asymmetric',
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'BraunBlanquet', 'Russel', 'RogotGoldberg'
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]:
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bulkSim = getattr(DataStructs, f'Bulk{metric}Similarity')
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nbrSim = getattr(DataStructs, f'{metric}SimilarityNeighbors')
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tgts = []
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for q in qs:
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sims = bulkSim(q, db)
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sim, idx = max((sim, -idx) for idx, sim in enumerate(sims))
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tgts.append((-idx, sim))
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nbrs = nbrSim(qs, db)
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self.assertEqual(tgts, nbrs)
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def test12ToList(self):
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nbits = 2048
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for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
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bv = cls(nbits)
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l = [0] * 2048
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# test no bits set
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l2 = list(bv)
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l3 = bv.ToList()
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self.assertEqual(l, l2)
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self.assertEqual(l, l3)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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l[x] = 1
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bv.SetBit(x)
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l2 = list(bv)
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l3 = bv.ToList()
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self.assertEqual(l, l2)
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self.assertEqual(l, l3)
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def test13Base64(self):
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nbits = 2048
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for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
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bv = cls(nbits)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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bv.SetBit(x)
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bv2 = cls(nbits)
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bv2.FromBase64(bv.ToBase64())
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self.assertEqual(bv, bv2)
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def test14NegativeIndices(self):
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nbits = 2048
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for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
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bv = cls(nbits)
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bv2 = cls(nbits)
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for _ in range(nbits):
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x = random.randrange(0, nbits)
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bv.SetBit(x)
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bv2[-(nbits - x)] = 1
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self.assertEqual(bv, bv2)
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for j in range(nbits):
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self.assertEqual(bv[j], bv[-(nbits - j)])
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with self.assertRaises(IndexError):
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bv[-(nbits + 1)]
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with self.assertRaises(IndexError):
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bv2[-(nbits + 1)] = 1
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def test15FoldFingerprint(self):
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for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
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fp = cls(8)
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fp[0] = 1
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fp[1] = 1
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fp[6] = 1
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ffp = DataStructs.FoldFingerprint(fp)
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self.assertTrue(ffp[0])
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self.assertTrue(ffp[1])
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self.assertTrue(ffp[2])
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self.assertFalse(ffp[3])
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if __name__ == '__main__':
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unittest.main()
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