def test8MultiFPBReaderContainsInitOnSearch(self): basen = os.path.join(RDConfig.RDBaseDir, 'Code', 'DataStructs', 'testData') mfpbr = DataStructs.MultiFPBReader(initOnSearch=True) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.1.patt.fpb"))), 1) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.2.patt.fpb"))), 2) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.3.patt.fpb"))), 3) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.4.patt.fpb"))), 4) fps = "40081010824820021000500010110410003000402b20285000a4040240010030050000"+\ "080001420040009000003d04086007080c03b31d920004220400074008098010206080"+\ "00488001080000c64002a00080000200024c2000602410049200340820200002400010"+\ "02200106090401056801080182006088101000088a0048" ebv = DataStructs.CreateFromFPSText(fps) bytes = DataStructs.BitVectToBinaryText(ebv) nbrs = mfpbr.GetContainingNeighbors(bytes, numThreads=4) self.assertEqual(len(nbrs), 9) self.assertEqual(nbrs[0][0], 160) self.assertEqual(nbrs[0][1], 0) self.assertEqual(nbrs[1][0], 163) self.assertEqual(nbrs[1][1], 0) self.assertEqual(nbrs[2][0], 170) self.assertEqual(nbrs[2][1], 0) self.assertEqual(nbrs[3][0], 180) self.assertEqual(nbrs[3][1], 2) self.assertEqual(nbrs[4][0], 182) self.assertEqual(nbrs[4][1], 3) self.assertEqual(nbrs[5][0], 185) self.assertEqual(nbrs[5][1], 0) self.assertEqual(nbrs[6][0], 189) self.assertEqual(nbrs[6][1], 0) self.assertEqual(nbrs[7][0], 192) self.assertEqual(nbrs[7][1], 3) self.assertEqual(nbrs[8][0], 193) self.assertEqual(nbrs[8][1], 0)
def test5Contains(self): " an example based on substructure screening " filename = os.path.join(RDConfig.RDBaseDir, 'Code', 'DataStructs', 'testData', 'zinc_all_clean.100.patt1k.fpb') fpbr = DataStructs.FPBReader(filename) fpbr.Init() bytes = b'\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00\x00\x00\x000\x00@\x00 \x00\x00 \x00\x00\x02@\x00\x00\x00\x00\x00\x00\x80\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00`\x07\x00\x04\x00"\x14\x02\x00\x00"\x00\x00\x00\x00\x08\x00\x80\x00\x00@\x00@\x00\x80\x00\x00\x00\x00B\x00\x00\x80\x00\x80\x08\x00\x04\x00@\x00\x00\x00\x00\x10\x00\x00\x00\x00\x00 \x00\x00\x00\x00\x00\x00\x00\x08\x00\x00\x00\x80\x04\x00\x00\x0c\x00\x00\x00@\x88\x10\x10\x00\x00\x88\x00@' nbrs = fpbr.GetContainingNeighbors(bytes) self.assertEqual(len(nbrs), 9) ids = sorted(fpbr.GetId(x) for x in nbrs) self.assertEqual(ids, [ 'ZINC00000562', 'ZINC00000843', 'ZINC00000969', 'ZINC00001484', 'ZINC00001585', 'ZINC00002094', 'ZINC00004739', 'ZINC00005235', 'ZINC00006300' ])
def test6MultiFPBReaderTani(self): basen = os.path.join(RDConfig.RDBaseDir, 'Code', 'DataStructs', 'testData') mfpbr = DataStructs.MultiFPBReader() self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.1.patt.fpb"))), 1) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.2.patt.fpb"))), 2) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.3.patt.fpb"))), 3) self.assertEqual( mfpbr.AddReader( DataStructs.FPBReader( os.path.join(basen, "zinc_random200.4.patt.fpb"))), 4) mfpbr.Init() self.assertEqual(mfpbr.GetNumBits(), 1024) self.assertEqual(len(mfpbr), 4) fps = "0000000000404000100000001000040000300040222000002004000240000020000000"+\ "8200010200000090000024040860070044003214820000220401054008018000226000"+\ "4800800140000042000080008008020482400000200410800000300430200800400000"+\ "0000080a0000800400010c800200648818100010880040" ebv = DataStructs.CreateFromFPSText(fps) bytes = DataStructs.BitVectToBinaryText(ebv) nbrs = mfpbr.GetTanimotoNeighbors(bytes, threshold=0.6) self.assertEqual(len(nbrs), 6) self.assertAlmostEqual(nbrs[0][0], 0.66412, 4) self.assertEqual(nbrs[0][1], 0) self.assertEqual(nbrs[0][2], 3) self.assertAlmostEqual(nbrs[1][0], 0.65289, 4) self.assertEqual(nbrs[1][1], 1) self.assertEqual(nbrs[1][2], 2) self.assertAlmostEqual(nbrs[2][0], 0.64341, 4) self.assertEqual(nbrs[2][1], 2) self.assertEqual(nbrs[2][2], 1) self.assertAlmostEqual(nbrs[3][0], 0.61940, 4) self.assertEqual(nbrs[3][1], 1) self.assertEqual(nbrs[3][2], 0) self.assertAlmostEqual(nbrs[4][0], 0.61905, 4) self.assertEqual(nbrs[4][1], 0) self.assertEqual(nbrs[4][2], 0) self.assertAlmostEqual(nbrs[5][0], 0.61344, 4) self.assertEqual(nbrs[5][1], 0) self.assertEqual(nbrs[5][2], 1) # test multi-threaded (won't do anything if the RDKit isn't compiled with threads support) nbrs = mfpbr.GetTanimotoNeighbors(bytes, threshold=0.6, numThreads=4) self.assertEqual(len(nbrs), 6) self.assertAlmostEqual(nbrs[0][0], 0.66412, 4) self.assertEqual(nbrs[0][1], 0) self.assertEqual(nbrs[0][2], 3) self.assertAlmostEqual(nbrs[1][0], 0.65289, 4) self.assertEqual(nbrs[1][1], 1) self.assertEqual(nbrs[1][2], 2) self.assertAlmostEqual(nbrs[2][0], 0.64341, 4) self.assertEqual(nbrs[2][1], 2) self.assertEqual(nbrs[2][2], 1) self.assertAlmostEqual(nbrs[3][0], 0.61940, 4) self.assertEqual(nbrs[3][1], 1) self.assertEqual(nbrs[3][2], 0) self.assertAlmostEqual(nbrs[4][0], 0.61905, 4) self.assertEqual(nbrs[4][1], 0) self.assertEqual(nbrs[4][2], 0) self.assertAlmostEqual(nbrs[5][0], 0.61344, 4) self.assertEqual(nbrs[5][1], 0) self.assertEqual(nbrs[5][2], 1)
def setUp(self): self.dirname = os.path.join(RDConfig.RDBaseDir, 'Code', 'DataStructs', 'testData') self.filename = os.path.join(self.dirname, 'zim.head100.fpb') self.fpbr = DataStructs.FPBReader(self.filename) self.fpbr.Init()