mirror of
https://github.com/rdkit/rdkit.git
synced 2026-06-07 22:44:25 +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
|
|
import random
|
|
import unittest
|
|
|
|
import numpy
|
|
|
|
from rdkit import DataStructs, RDConfig
|
|
|
|
|
|
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.assertTrue(bv1 == bv2)
|
|
bv2.SetBit(1)
|
|
self.assertTrue(bv1 != bv2)
|
|
bv2.UnSetBit(1)
|
|
self.assertTrue(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]
|
|
with self.assertRaisesRegex(IndexError, ""):
|
|
bv1[11]
|
|
|
|
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.assertTrue(DataStructs.AllProbeBitsMatch(bv1, bv1.ToBinary()))
|
|
self.assertTrue(DataStructs.AllProbeBitsMatch(bv2, bv1.ToBinary()))
|
|
self.assertFalse(DataStructs.AllProbeBitsMatch(bv1, bv2.ToBinary()))
|
|
self.assertTrue(DataStructs.AllProbeBitsMatch(bv2, bv2.ToBinary()))
|
|
|
|
def test5FromBitString(self):
|
|
s1 = '1010'
|
|
bv = DataStructs.CreateFromBitString(s1)
|
|
self.assertTrue(len(bv) == 4)
|
|
self.assertTrue(list(bv.GetOnBits()) == [0, 2])
|
|
|
|
def _bulkTest(self, bvs):
|
|
for metric in 'Tanimoto', 'Dice', 'AllBit', 'OnBit', 'RogotGoldberg':
|
|
bulk = getattr(DataStructs, f'Bulk{metric}Similarity')
|
|
single = getattr(DataStructs, f'{metric}Similarity')
|
|
sims = bulk(bvs[0], bvs)
|
|
for i, bbvs in enumerate(bvs):
|
|
sim = single(bvs[0], bbvs)
|
|
self.assertEqual(sim, sims[i])
|
|
self.assertEqual(sim, single(bvs[0], bbvs.ToBinary()))
|
|
dists = bulk(bvs[0], bvs, returnDistance=True)
|
|
for i, bbvs in enumerate(bvs):
|
|
dist = single(bvs[0], bbvs, returnDistance=True)
|
|
self.assertEqual(dist, dists[i])
|
|
self.assertEqual(dist, single(bvs[0], bbvs.ToBinary(), returnDistance=True))
|
|
|
|
sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1)
|
|
for i, bbvs in enumerate(bvs):
|
|
sim = DataStructs.TverskySimilarity(bvs[0], bbvs, 1, 1)
|
|
self.assertEqual(sim, sims[i])
|
|
sim = DataStructs.TanimotoSimilarity(bvs[0], bbvs)
|
|
self.assertEqual(sim, sims[i])
|
|
|
|
sims = DataStructs.BulkTverskySimilarity(bvs[0], bvs, 1, 1, returnDistance=True)
|
|
for i, bbvs in enumerate(bvs):
|
|
sim = DataStructs.TverskySimilarity(bvs[0], bbvs, 1, 1, returnDistance=True)
|
|
self.assertEqual(sim, sims[i])
|
|
sim = DataStructs.TanimotoSimilarity(bvs[0], bbvs, returnDistance=True)
|
|
self.assertEqual(sim, sims[i])
|
|
|
|
def test6BulkOps(self):
|
|
nbits = 10000
|
|
bvs = []
|
|
for _ in range(10):
|
|
bv = DataStructs.ExplicitBitVect(nbits)
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
bv.SetBit(x)
|
|
bvs.append(bv)
|
|
self._bulkTest(bvs)
|
|
|
|
def test10BulkOps2(self):
|
|
nbits = 10000
|
|
bvs = []
|
|
for _ in range(10):
|
|
bv = DataStructs.ExplicitBitVect(nbits)
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
bv.SetBit(x)
|
|
bvs.append(bv)
|
|
bvs = tuple(bvs)
|
|
self._bulkTest(bvs)
|
|
|
|
def test10BulkOps3(self):
|
|
nbits = 10000
|
|
bvs = numpy.empty((10, ), DataStructs.ExplicitBitVect)
|
|
for bvi in range(10):
|
|
bv = DataStructs.ExplicitBitVect(nbits)
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
bv.SetBit(x)
|
|
bvs[bvi] = bv
|
|
self._bulkTest(bvs)
|
|
|
|
def test7FPS(self):
|
|
bv = DataStructs.ExplicitBitVect(32)
|
|
bv.SetBit(0)
|
|
bv.SetBit(1)
|
|
bv.SetBit(17)
|
|
bv.SetBit(23)
|
|
bv.SetBit(31)
|
|
|
|
self.assertEqual(DataStructs.BitVectToFPSText(bv), "03008280")
|
|
bv2 = DataStructs.CreateFromFPSText("03008280")
|
|
self.assertEqual(bv, bv2)
|
|
|
|
self.assertRaises(ValueError, lambda: DataStructs.CreateFromFPSText("030082801"))
|
|
|
|
bv2 = DataStructs.CreateFromFPSText("")
|
|
self.assertEqual(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.assertEqual(bv, bv2)
|
|
|
|
bv2 = DataStructs.CreateFromBinaryText("")
|
|
self.assertEqual(bv2.GetNumBits(), 0)
|
|
|
|
def test9ToNumpy(self):
|
|
import numpy
|
|
for typ in (DataStructs.ExplicitBitVect, ):
|
|
bv = typ(32)
|
|
bv.SetBit(0)
|
|
bv.SetBit(1)
|
|
bv.SetBit(17)
|
|
bv.SetBit(23)
|
|
bv.SetBit(31)
|
|
arr = numpy.zeros((32, ), 'i')
|
|
DataStructs.ConvertToNumpyArray(bv, arr)
|
|
for i in range(bv.GetNumBits()):
|
|
self.assertEqual(bv[i], arr[i])
|
|
|
|
for typ in (DataStructs.IntSparseIntVect, DataStructs.LongSparseIntVect,
|
|
DataStructs.UIntSparseIntVect, DataStructs.ULongSparseIntVect):
|
|
iv = typ(32)
|
|
iv[0] = 1
|
|
iv[1] = 1
|
|
iv[17] = 1
|
|
iv[23] = 1
|
|
iv[31] = 1
|
|
arr = numpy.zeros((32, ), 'i')
|
|
DataStructs.ConvertToNumpyArray(iv, arr)
|
|
for i in range(iv.GetLength()):
|
|
self.assertEqual(iv[i], arr[i])
|
|
|
|
def test11BulkNeighbors(self):
|
|
nbits = 2048
|
|
bvs = []
|
|
for _ in range(1000):
|
|
bv = DataStructs.ExplicitBitVect(nbits)
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
bv.SetBit(x)
|
|
bvs.append(bv)
|
|
qs = bvs[:10]
|
|
db = bvs[10:]
|
|
for metric in [
|
|
'Tanimoto', 'Cosine', 'Kulczynski', 'Dice', 'Sokal', 'McConnaughey', 'Asymmetric',
|
|
'BraunBlanquet', 'Russel', 'RogotGoldberg'
|
|
]:
|
|
bulkSim = getattr(DataStructs, f'Bulk{metric}Similarity')
|
|
nbrSim = getattr(DataStructs, f'{metric}SimilarityNeighbors')
|
|
tgts = []
|
|
for q in qs:
|
|
sims = bulkSim(q, db)
|
|
sim, idx = max((sim, -idx) for idx, sim in enumerate(sims))
|
|
tgts.append((-idx, sim))
|
|
nbrs = nbrSim(qs, db)
|
|
self.assertEqual(tgts, nbrs)
|
|
|
|
def test12ToList(self):
|
|
nbits = 2048
|
|
for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
|
|
bv = cls(nbits)
|
|
l = [0] * 2048
|
|
|
|
# test no bits set
|
|
l2 = list(bv)
|
|
l3 = bv.ToList()
|
|
self.assertEqual(l, l2)
|
|
self.assertEqual(l, l3)
|
|
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
l[x] = 1
|
|
bv.SetBit(x)
|
|
|
|
l2 = list(bv)
|
|
l3 = bv.ToList()
|
|
self.assertEqual(l, l2)
|
|
self.assertEqual(l, l3)
|
|
|
|
def test13Base64(self):
|
|
nbits = 2048
|
|
for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
|
|
bv = cls(nbits)
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
bv.SetBit(x)
|
|
|
|
bv2 = cls(nbits)
|
|
bv2.FromBase64(bv.ToBase64())
|
|
self.assertEqual(bv, bv2)
|
|
|
|
def test14NegativeIndices(self):
|
|
nbits = 2048
|
|
for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
|
|
bv = cls(nbits)
|
|
bv2 = cls(nbits)
|
|
for _ in range(nbits):
|
|
x = random.randrange(0, nbits)
|
|
bv.SetBit(x)
|
|
bv2[-(nbits - x)] = 1
|
|
|
|
self.assertEqual(bv, bv2)
|
|
for j in range(nbits):
|
|
self.assertEqual(bv[j], bv[-(nbits - j)])
|
|
with self.assertRaises(IndexError):
|
|
bv[-(nbits + 1)]
|
|
with self.assertRaises(IndexError):
|
|
bv2[-(nbits + 1)] = 1
|
|
|
|
def test15FoldFingerprint(self):
|
|
for cls in [DataStructs.ExplicitBitVect, DataStructs.SparseBitVect]:
|
|
fp = cls(8)
|
|
fp[0] = 1
|
|
fp[1] = 1
|
|
fp[6] = 1
|
|
ffp = DataStructs.FoldFingerprint(fp)
|
|
self.assertTrue(ffp[0])
|
|
self.assertTrue(ffp[1])
|
|
self.assertTrue(ffp[2])
|
|
self.assertFalse(ffp[3])
|
|
|
|
|
|
if __name__ == '__main__':
|
|
unittest.main()
|