def test2(self):
""" test RIE """
ratio = float(self.numActives) / self.numMol
# best case
RIEmax = ((1 - math.exp(-self.alpha*ratio)) / (1 - math.exp(-self.alpha))) / ratio
rie = Scoring.CalcRIE(self.scoreBestCase, self.index, self.alpha)
self.assertAlmostEqual(rie, RIEmax, self.acc)
# worst case
RIEmin = ((1 - math.exp(self.alpha*ratio)) / (1 - math.exp(self.alpha))) / ratio
rie = Scoring.CalcRIE(self.scoreWorstCase, self.index, self.alpha)
self.assertAlmostEqual(rie, RIEmin, self.acc)
# empty list
self.assertRaises(ValueError, Scoring.CalcRIE, self.scoreEmptyList, self.index, self.alpha)
# alpha == 0
self.assertRaises(ValueError, Scoring.CalcRIE, self.scoreBestCase, self.index, 0.0)
# all decoys
rie = Scoring.CalcRIE(self.scoreAllDecoys, self.index, self.alpha)
self.assertEqual(rie, 0.0)
def evaluate(activity_arr):
auc = Scoring.CalcAUC(activity_arr, 0)
print("AUC: ", auc)
ef = Scoring.CalcEnrichment(activity_arr, 0, [0.01])
print("EF for 1%: ", ef[0])
ef = Scoring.CalcEnrichment(activity_arr, 0, [0.05])
print("EF for 5%: ", ef[0])
rie = Scoring.CalcRIE(activity_arr, 0, 100)
print("RIE for 100: ", rie)
bedroc = Scoring.CalcBEDROC(activity_arr, 0, 100)
print("BEDROC for 100: ", bedroc)
def evaluation(activity_arr: list, output_file: str):
inputoutput_utils.create_parent_directory(output_file)
auc = Scoring.CalcAUC(activity_arr, 0)
ef1 = Scoring.CalcEnrichment(activity_arr, 0, [0.01])
ef5 = Scoring.CalcEnrichment(activity_arr, 0, [0.05])
rie = Scoring.CalcRIE(activity_arr, 0, 100)
bedroc = Scoring.CalcBEDROC(activity_arr, 0, 100)
output = {
"AUC": auc,
"EF1": ef1[0],
"EF5": ef5[0],
"RIE": rie,
"BEDROC": bedroc
}
with open(output_file, "w", encoding="utf-8") as stream:
json.dump(output, stream)
def evaluation(activity_arr: list, output_file: str):
with open(output_file, "w") as stream:
auc = Scoring.CalcAUC(activity_arr, 0)
stream.write("AUC: ")
stream.write(str(auc))
ef = Scoring.CalcEnrichment(activity_arr, 0, [0.01])
stream.write("\nEF for 1%: ")
stream.write(str(ef[0]))
ef = Scoring.CalcEnrichment(activity_arr, 0, [0.05])
stream.write("\nEF for 5%: ")
stream.write(str(ef[0]))
rie = Scoring.CalcRIE(activity_arr, 0, 100)
stream.write("\nRIE for 100: ")
stream.write(str(rie))
bedroc = Scoring.CalcBEDROC(activity_arr, 0, 100)
stream.write("\nBEDROC for 100: ")
stream.write(str(bedroc))
def calculate(self, score, index):
tmp = []
for p in self.params:
tmp.append(Scoring.CalcRIE(score, index, p))
return tmp