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from rdkit import RDConfig
import unittest, os
from rdkit.SimDivFilters import rdSimDivPickers
from rdkit.DataManip.Metric import rdMetricMatrixCalc as rdmmc
from rdkit import DataStructs
import numpy
import random
class TestCase(unittest.TestCase):
def setUp(self):
self.n = 1000
self.m = 80
self.d = 2
self.dataPts = numpy.zeros((self.n, self.d), 'd')
for i in range(self.n):
for j in range(self.d):
self.dataPts[i, j] = random.random()
self.dMat = rdmmc.GetEuclideanDistMat(self.dataPts)
def test0MaxMin(self):
pkr = rdSimDivPickers.MaxMinPicker()
maxmin = pkr.Pick(self.dMat, self.n, self.m, (886, 112))
self.assertEqual(maxmin[0], 886)
self.assertEqual(maxmin[1], 112)
def func(i, j):
if i == j:
return 0.0
if i < j:
j, i = i, j
return self.dMat[i * (i - 1) // 2 + j]
lmaxmin = pkr.LazyPick(func, self.n, self.m, (886, 112))
self.assertEqual(list(lmaxmin), list(maxmin))
lmaxmin = pkr.LazyPick(func, self.n, self.m, (886, 112), useCache=False)
self.assertEqual(list(lmaxmin), list(maxmin))
self.assertRaises(ValueError, lambda: pkr.Pick(self.dMat, self.n, self.m, (1012, )))
self.assertRaises(ValueError, lambda: pkr.Pick(self.dMat, self.n, self.m, (-1, )))
maxmin = pkr.Pick(self.dMat, self.n, self.m)
self.assertTrue(maxmin)
lmaxmin = pkr.LazyPick(func, self.n, self.m)
self.assertTrue(lmaxmin)
def test1HierarchPick(self):
fname = os.path.join(RDConfig.RDBaseDir, 'Code', 'SimDivPickers', 'Wrap', 'test_data',
'points.csv')
with open(fname) as infil:
lines = infil.readlines()
self.dataPts = numpy.zeros((len(lines), 2), 'd')
labels = []
i = 0
for line in lines:
tlst = line.strip().split(',')
self.dataPts[i, 0] = float(tlst[1])
self.dataPts[i, 1] = float(tlst[2])
labels.append(int(tlst[3]))
i += 1
self.dMat = rdmmc.GetEuclideanDistMat(self.dataPts)
pkr = rdSimDivPickers.HierarchicalClusterPicker(rdSimDivPickers.ClusterMethod.WARD)
clusters = pkr.Cluster(self.dMat, i, 2)
# check that each of the clusters have the same label
for cl in clusters:
clbl = labels[cl[0]]
for id in cl:
assert clbl == labels[id]
hierarch = pkr.Pick(self.dMat, i, 2)
self.assertEqual(tuple(hierarch), (1, 30))
def testIssue208(self):
sz = 10
N = 3
m = []
for i in range(sz):
for j in range(i + 1, sz):
m.append(random.random())
m = numpy.array(m)
picker = rdSimDivPickers.HierarchicalClusterPicker(rdSimDivPickers.ClusterMethod.WARD)
p1 = list(picker.Pick(m, sz, N))
p1.sort()
p2 = list(picker.Pick(m, sz, N))
p2.sort()
self.assertEqual(p1, p2)
def testInts(self):
""" make sure we can handle ints too """
sz = 10
N = 3
m = []
for i in range(sz):
for j in range(i + 1, sz):
m.append(int(100 * random.random()))
m = numpy.array(m)
picker = rdSimDivPickers.HierarchicalClusterPicker(rdSimDivPickers.ClusterMethod.WARD)
p1 = list(picker.Pick(m, sz, N))
p1.sort()
p2 = list(picker.Pick(m, sz, N))
p2.sort()
self.assertEqual(p1, p2)
def testNonUniqueCrash(self):
from rdkit import DataStructs
sz = 10
nbits = 20
nBitsToSet = int(nbits * .3)
N = 12
vs = []
for i in range(sz):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nBitsToSet):
val = int(nbits * random.random())
bv.SetBit(val)
vs.append(bv)
vs.append(bv)
def taniFunc(i, j, bvs=vs):
d = 1 - DataStructs.FingerprintSimilarity(bvs[i], bvs[j])
return d
picker = rdSimDivPickers.MaxMinPicker()
mm1 = picker.LazyPick(taniFunc, len(vs), N)
self.assertEqual(len(mm1), N)
picker = None
picker = rdSimDivPickers.MaxMinPicker()
mm2 = picker.LazyBitVectorPick(vs, len(vs), N)
self.assertEqual(len(mm2), N)
self.assertEqual(tuple(mm2), tuple(mm1))
picker = None
ds = []
nvs = len(vs)
for i in range(nvs):
for j in range(i + 1, nvs):
d = taniFunc(i, j)
ds.append(d)
m = numpy.array(ds)
picker = rdSimDivPickers.HierarchicalClusterPicker(rdSimDivPickers.ClusterMethod.WARD)
p1 = list(picker.Pick(m, nvs, N))
def testBitVectorMaxMin(self):
from rdkit import DataStructs
sz = 100
nbits = 200
nBitsToSet = int(nbits * .1)
N = 10
vs = []
for i in range(sz):
bv = DataStructs.ExplicitBitVect(nbits)
for j in range(nBitsToSet):
val = int(nbits * random.random())
bv.SetBit(val)
vs.append(bv)
def func(i, j, bvs=vs):
d = DataStructs.TanimotoSimilarity(bvs[i], bvs[j], returnDistance=True)
return d
picker = rdSimDivPickers.MaxMinPicker()
mm1 = picker.LazyPick(func, len(vs), N)
self.assertEqual(len(mm1), N)
mm2 = picker.LazyPick(func, len(vs), N, useCache=False)
self.assertEqual(len(mm2), N)
self.assertEqual(list(mm1), list(mm2))
mm2 = picker.LazyBitVectorPick(vs, len(vs), N)
self.assertEqual(len(mm2), N)
self.assertEqual(list(mm1), list(mm2))
mm2 = picker.LazyBitVectorPick(vs, len(vs), N, useCache=False)
self.assertEqual(len(mm2), N)
self.assertEqual(list(mm1), list(mm2))
def testBitVectorMaxMin2(self):
fps = ["11110010101000000000", "00000000000010010000", "11001010000000000001",
"00100110101000001000", "01010110000100011001", "11000110101001000011",
"00000000001100001111", "00011110110000001101", "00000011011110100010",
"11000010110001000000", "00000100010000010000", "10000001000010110010",
"00010010000000010100", "00011100100110101000", "10001001100110100000",
"10000110100110010000", "00101110000101000000", "11011101100011100000",
"10000110000100101000", "00101000100000010001", "01000001000010000000",
"00101101010100000110", "10001000100110110001", "00011000010100000001",
"00101000001000100011", "00010000100010011001", "01100001000100010001",
"10000101000001101101", "00001000011001011000", "11110000100100100000",
"10100110000000011010", "00110100010110010010", "00000000000001010010",
"00100000000010100001", "11110011000010001000", "10110001010100001000",
"00001100100110011011", "00010010100100001110", "10100101100010100010",
"01100100010100000001", "10101110011100000000", "01011000000001000001",
"00000011100110100010", "01100001010001001001", "00001000000001001100",
"10011001110000000100", "10110000001001100100", "00011000000001001011",
"11001011010001100010", "10010000000001001011", "00010000100111100000",
"00001000001110001000", "11010000010001100110", "01101001100000111000",
"01001000001110111000", "10000000000100010010", "11001000010010000000",
"01010010000100110001", "00010001010100100001", "01110010000000010000",
"10001010000011000001", "00000110000000100100", "00010000010001000000",
"11101100011010000011", "00000010100001010001", "00010000110010000101",
"00010001001000111001", "01000010001100100110", "00110110000000100001",
"00100010010110110010", "01000000110011001111", "00011000001000110010",
"01111010101000110100", "00001010000010110110", "00110011000011011010",
"00111010111010000110", "00010011101010000011", "00000001011000010000",
"00011011101110110000", "00010001101000000001", "00010000001010011010",
"00000010100100100010", "00000010001011000100", "11010000000001011100",
"00001000110101000001", "00000010000000110010", "10000000010011000001",
"11110110100100010000", "10001111000110001001", "00100110000110000100",
"00000100100000100100", "00110000101100010100", "00001010100000100000",
"01011000000011000111", "00010000100001010001", "10000010100000010000",
"00001000000000110010", "00001000101011010001", "00011110000100100000",
"11001001010001010100"]
N = 5
fps = [DataStructs.CreateFromBitString(x) for x in fps]
picker = rdSimDivPickers.MaxMinPicker()
mm1 = picker.LazyBitVectorPick(fps, len(fps), N)
self.assertEqual(len(mm1), N)
self.assertEqual(list(mm1), [37, 1, 43, 38, 16])
mm2 = picker.LazyBitVectorPick(fps, len(fps), N, useCache=False)
self.assertEqual(len(mm2), N)
self.assertEqual(list(mm1), list(mm2))
def testBitVectorMaxMin3(self):
fname = os.path.join(RDConfig.RDBaseDir, 'Code', 'SimDivPickers', 'Wrap', 'test_data',
'chembl_cyps.head.fps')
fps = []
with open(fname) as infil:
for line in infil:
fp = DataStructs.CreateFromFPSText(line.strip())
fps.append(fp)
mmp =rdSimDivPickers.MaxMinPicker()
ids=list(mmp.LazyBitVectorPick(fps,len(fps),20))
self.assertEqual(ids,[374,720,690,339,875,842,404,725,120,385,115,868,630,\
881,516,497,412,718,869,407])
ids=list(mmp.LazyBitVectorPick(fps,len(fps),20,firstPicks=[374,720,690,339,875]))
self.assertEqual(ids,[374,720,690,339,875,842,404,725,120,385,115,868,630,\
881,516,497,412,718,869,407])
def testBitVectorMaxMin4(self):
# threshold tests
fname = os.path.join(RDConfig.RDBaseDir, 'Code', 'SimDivPickers', 'Wrap', 'test_data',
'chembl_cyps.head.fps')
fps = []
with open(fname) as infil:
for line in infil:
fp = DataStructs.CreateFromFPSText(line.strip())
fps.append(fp)
mmp =rdSimDivPickers.MaxMinPicker()
ids,threshold=mmp.LazyBitVectorPickWithThreshold(fps,len(fps),20,-1.0)
self.assertEqual(list(ids),[374,720,690,339,875,842,404,725,120,385,115,868,630,\
881,516,497,412,718,869,407])
self.assertAlmostEqual(threshold,0.8977,4)
ids,threshold=mmp.LazyBitVectorPickWithThreshold(fps,len(fps),20,0.91)
self.assertEqual(list(ids),[374,720,690,339,875,842,404,725,120,385,115,868,630])
self.assertTrue(threshold>=0.91)
if __name__ == '__main__':
unittest.main()
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