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]))