def computeSimilarityFP(self, c_chem, typeFP, typeMetric): try: if typeMetric == 'Tanimoto': return DataStructs.TanimotoSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "Dice": return DataStructs.DiceSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "Cosine": return DataStructs.CosineSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "Sokal": return DataStructs.SokalSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "Russel": return DataStructs.RusselSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "RogotGoldberg": return DataStructs.RogotGoldbergSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "AllBit": return DataStructs.AllBitSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "Kulczynski": return DataStructs.KulczynskiSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "McConnaughey": return DataStructs.McConnaugheySimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "Asymmetric": return DataStructs.AsymmetricSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) elif typeMetric == "BraunBlanquet": return DataStructs.BraunBlanquetSimilarity(self.d_FP[typeFP], c_chem.d_FP[typeFP]) except: print("Combination %s and %s not supported"%(typeFP, typeMetric)) self.log = "%sCombination %s and %s not supported\n"%(self.log, typeFP, typeMetric) return "NA"
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.assertTrue(feq(sim, sims[i])) sims = DataStructs.BulkDiceSimilarity(bvs[0], bvs) for i in range(len(bvs)): sim = DataStructs.DiceSimilarity(bvs[0], bvs[i]) self.assertTrue(feq(sim, sims[i])) sims = DataStructs.BulkAllBitSimilarity(bvs[0], bvs) for i in range(len(bvs)): sim = DataStructs.AllBitSimilarity(bvs[0], bvs[i]) self.assertTrue(feq(sim, sims[i])) sims = DataStructs.BulkOnBitSimilarity(bvs[0], bvs) for i in range(len(bvs)): sim = DataStructs.OnBitSimilarity(bvs[0], bvs[i]) self.assertTrue(feq(sim, sims[i])) sims = DataStructs.BulkRogotGoldbergSimilarity(bvs[0], bvs) for i in range(len(bvs)): sim = DataStructs.RogotGoldbergSimilarity(bvs[0], bvs[i]) self.assertTrue(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.assertTrue(feq(sim, sims[i])) sim = DataStructs.TanimotoSimilarity(bvs[0], bvs[i]) self.assertTrue(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.assertTrue(feq(sim, sims[i])) sim = DataStructs.DiceSimilarity(bvs[0], bvs[i]) self.assertTrue(feq(sim, sims[i]))