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()