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* Issue #1071: add yapf configuration file * yapf formatting of Code directory * yapf formatting of Contrib directory * yapf formatting of Data directory * yapf formatting of Docs directory * yapf formatting of External directory * yapf formatting of Projects directory * yapf formatting of Regress directory * yapf formatting of Scripts directory * yapf formatting of Web directory * yapf formatting of rdkit directory
304 lines
9.1 KiB
Python
Executable File
304 lines
9.1 KiB
Python
Executable File
from rdkit import DataStructs
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from rdkit import RDConfig
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import unittest
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from rdkit.six.moves import cPickle as pickle
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import random
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import numpy
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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.assertRaisesRegexp(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 test6BulkOps(self):
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nbits = 10000
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bvs = []
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for bvi in range(10):
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bv = DataStructs.ExplicitBitVect(nbits)
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for j 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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sims = DataStructs.BulkTanimotoSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkDiceSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkAllBitSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.AllBitSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkOnBitSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.OnBitSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.RogotGoldbergSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
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for i in range(len(bvs)):
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sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], 1, 1)
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self.assertTrue(feq(sim, sims[i]))
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sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, .5, .5)
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for i in range(len(bvs)):
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sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], .5, .5)
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self.assertTrue(feq(sim, sims[i]))
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sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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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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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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arr = numpy.zeros((3, ), '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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def test10BulkOps2(self):
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nbits = 10000
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bvs = []
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for bvi in range(10):
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bv = DataStructs.ExplicitBitVect(nbits)
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for j 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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sims = DataStructs.BulkTanimotoSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkDiceSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkAllBitSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.AllBitSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkOnBitSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.OnBitSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.RogotGoldbergSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
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for i in range(len(bvs)):
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sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], 1, 1)
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self.assertTrue(feq(sim, sims[i]))
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sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, .5, .5)
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for i in range(len(bvs)):
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sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], .5, .5)
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self.assertTrue(feq(sim, sims[i]))
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sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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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 j 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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sims = DataStructs.BulkTanimotoSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkDiceSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkAllBitSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.AllBitSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkOnBitSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.OnBitSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0], bvs)
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for i in range(len(bvs)):
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sim = DataStructs.RogotGoldbergSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
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for i in range(len(bvs)):
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sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], 1, 1)
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self.assertTrue(feq(sim, sims[i]))
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sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, .5, .5)
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for i in range(len(bvs)):
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sim = DataStructs.TverskySimilarity(bvs[0], bvs[i], .5, .5)
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self.assertTrue(feq(sim, sims[i]))
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sim = DataStructs.DiceSimilarity(bvs[0], bvs[i])
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self.assertTrue(feq(sim, sims[i]))
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if __name__ == '__main__':
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unittest.main()
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