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from rdkit import DataStructs
from rdkit import RDConfig
import unittest
import cPickle as pickle
import random
import numpy
def feq(a,b,tol=1e-4):
return abs(a-b)<tol
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test0FromList(self) :
bv1 = DataStructs.SparseBitVect(1000)
bv2 = DataStructs.SparseBitVect(1000)
obits = range(0,1000, 3)
for bit in obits :
bv1.SetBit(bit)
bv2.SetBitsFromList(obits)
for i in range(1000) :
assert bv1.GetBit(i) == bv2.GetBit(i)
self.failUnless(bv1==bv2)
bv2.SetBit(1)
self.failUnless(bv1!=bv2)
bv2.UnSetBit(1)
self.failUnless(bv1==bv2)
bv2.UnSetBitsFromList(obits)
for i in range(1000) :
assert bv2.GetBit(i) == 0
bv1 = DataStructs.ExplicitBitVect(1000)
bv2 = DataStructs.ExplicitBitVect(1000)
obits = range(0,1000, 3)
for bit in obits :
bv1.SetBit(bit)
bv2.SetBitsFromList(obits)
for i in range(1000) :
assert bv1.GetBit(i) == bv2.GetBit(i)
bv2.UnSetBitsFromList(obits)
for i in range(1000) :
assert bv2.GetBit(i) == 0
def test01BVWithAllOnes(self) :
bv1 = DataStructs.ExplicitBitVect(10, True)
for i in range(10) :
assert bv1.GetBit(i) == 1
def test1SparsePickle(self) :
nbits = 10000
bv1 = DataStructs.SparseBitVect(nbits)
for i in range(1000) :
x = random.randrange(0,nbits)
bv1.SetBit(x)
pkl = pickle.dumps(bv1,1)
bv2 = pickle.loads(pkl)
for i in range(nbits) :
assert bv1[i] == bv2[i]
def test2ExplicitPickle(self):
nbits = 10000
bv1 = DataStructs.ExplicitBitVect(nbits)
for i in range(1000) :
x = random.randrange(0,nbits)
bv1.SetBit(x)
pkl = pickle.dumps(bv1,1)
bv2 = pickle.loads(pkl)
for i in range(nbits) :
assert bv1[i] == bv2[i]
def test3Bounds(self) :
nbits = 10
bv1 = DataStructs.ExplicitBitVect(nbits)
bv1[0]
try:
bv1[11]
except IndexError:
ok = 1
except:
ok = -1
else:
ok = 0
assert ok>0,ok
def test4OnBitsInCommon(self) :
sz=100
bv1 = DataStructs.ExplicitBitVect(sz)
bv2 = DataStructs.ExplicitBitVect(sz)
for i in range(0,sz,2):
bv1.SetBit(i)
if i < 3*sz/4:
bv2.SetBit(i)
self.failUnless(DataStructs.AllProbeBitsMatch(bv1,bv1.ToBinary()))
self.failUnless(DataStructs.AllProbeBitsMatch(bv2,bv1.ToBinary()))
self.failIf(DataStructs.AllProbeBitsMatch(bv1,bv2.ToBinary()))
self.failUnless(DataStructs.AllProbeBitsMatch(bv2,bv2.ToBinary()))
def test5FromBitString(self):
s1 = '1010'
bv = DataStructs.CreateFromBitString(s1)
self.failUnless(len(bv)==4)
self.failUnless(list(bv.GetOnBits())==[0,2])
def test6BulkOps(self):
nbits = 10000
bvs = []
for bvi in range(10):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nbits) :
x = random.randrange(0,nbits)
bv.SetBit(x)
bvs.append(bv)
sims = DataStructs.BulkTanimotoSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.TanimotoSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkDiceSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.DiceSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkAllBitSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.AllBitSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkOnBitSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.OnBitSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.RogotGoldbergSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0],bvs,1,1)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0],bvs[i],1,1)
self.failUnless(feq(sim,sims[i]))
sim = DataStructs.TanimotoSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0],bvs,.5,.5)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0],bvs[i],.5,.5)
self.failUnless(feq(sim,sims[i]))
sim = DataStructs.DiceSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
def test7FPS(self):
bv = DataStructs.ExplicitBitVect(32)
bv.SetBit(0)
bv.SetBit(1)
bv.SetBit(17)
bv.SetBit(23)
bv.SetBit(31)
self.failUnlessEqual(DataStructs.BitVectToFPSText(bv),"03008280")
bv2 = DataStructs.CreateFromFPSText("03008280")
self.failUnlessEqual(bv,bv2)
self.failUnlessRaises(ValueError,lambda : DataStructs.CreateFromFPSText("030082801"))
bv2 = DataStructs.CreateFromFPSText("")
self.failUnlessEqual(bv2.GetNumBits(),0)
def test8BinText(self):
bv = DataStructs.ExplicitBitVect(32)
bv.SetBit(0)
bv.SetBit(1)
bv.SetBit(17)
bv.SetBit(23)
bv.SetBit(31)
bv2 = DataStructs.CreateFromBinaryText(DataStructs.BitVectToBinaryText(bv))
self.failUnlessEqual(bv,bv2)
bv2 = DataStructs.CreateFromBinaryText("")
self.failUnlessEqual(bv2.GetNumBits(),0)
def test9ToNumpy(self):
import numpy
bv = DataStructs.ExplicitBitVect(32)
bv.SetBit(0)
bv.SetBit(1)
bv.SetBit(17)
bv.SetBit(23)
bv.SetBit(31)
arr = numpy.zeros((3,),'i')
DataStructs.ConvertToNumpyArray(bv,arr)
for i in range(bv.GetNumBits()):
self.failUnlessEqual(bv[i],arr[i])
def test10BulkOps2(self):
nbits = 10000
bvs = []
for bvi in range(10):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nbits) :
x = random.randrange(0,nbits)
bv.SetBit(x)
bvs.append(bv)
bvs = tuple(bvs)
sims = DataStructs.BulkTanimotoSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.TanimotoSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkDiceSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.DiceSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkAllBitSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.AllBitSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkOnBitSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.OnBitSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.RogotGoldbergSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0],bvs,1,1)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0],bvs[i],1,1)
self.failUnless(feq(sim,sims[i]))
sim = DataStructs.TanimotoSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0],bvs,.5,.5)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0],bvs[i],.5,.5)
self.failUnless(feq(sim,sims[i]))
sim = DataStructs.DiceSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
def test10BulkOps3(self):
nbits = 10000
bvs = numpy.empty((10,),DataStructs.ExplicitBitVect)
for bvi in range(10):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nbits) :
x = random.randrange(0,nbits)
bv.SetBit(x)
bvs[bvi]=bv
sims = DataStructs.BulkTanimotoSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.TanimotoSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkDiceSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.DiceSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkAllBitSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.AllBitSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkOnBitSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.OnBitSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0],bvs)
for i in range(len(bvs)):
sim = DataStructs.RogotGoldbergSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0],bvs,1,1)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0],bvs[i],1,1)
self.failUnless(feq(sim,sims[i]))
sim = DataStructs.TanimotoSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
sims = DataStructs.BulkTverskySimilarity(bvs[0],bvs,.5,.5)
for i in range(len(bvs)):
sim = DataStructs.TverskySimilarity(bvs[0],bvs[i],.5,.5)
self.failUnless(feq(sim,sims[i]))
sim = DataStructs.DiceSimilarity(bvs[0],bvs[i])
self.failUnless(feq(sim,sims[i]))
if __name__ == '__main__':
unittest.main()
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