def hide_test_getCinfonyDesc(self):
allDescs = getCinfonyDesc.getAvailableDescs()
print "\nN Retrieved desc: ",len(allDescs)
self.assert_(len(allDescs) > 200) # Actualy 220
descs = ['cdk.BCUT', 'cdk.weight','webel.AtomCountDescriptor', 'webel.AutocorrelationDescriptorCharge', 'webel.AutocorrelationDescriptorMass',"obabel.TPSA","obabel.HBA2" , "obabel.MW","rdk.TPSA","rdk.Chi0n","rdk.MolWt"]
resD = getCinfonyDesc.getCinfonyDescResults(self.smiData,descs)
self.assertEqual(len(resD),len(self.smiData))
def test_getCinfonyDesc(self):
allDescs = getCinfonyDesc.getAvailableDescs()
print "\nN Retrieved desc: ",len(allDescs)
self.assert_(len(allDescs) > 200) # Actualy 220
descs = ['cdk.BCUT', 'cdk.weight','webel.AtomCountDescriptor', 'webel.AutocorrelationDescriptorCharge', 'webel.AutocorrelationDescriptorMass',"obabel.TPSA","obabel.HBA2" , "obabel.MW","rdk.TPSA","rdk.Chi0n","rdk.MolWt"]
resD = getCinfonyDesc.getCinfonyDescResults(self.smiData,descs)
self.assertEqual(len(resD),len(self.smiData))
def getDescriptors(self, smiles):
self.getSmilesData(smiles)
# Calculate descriptors defined in the model files
descList = self.model.varNames
savedSmilesData = dataUtilities.DataTable(self.smilesData)
#Try 3 time to get All compounds descriptors
nTry = 3
errorDesc = ""
while nTry > 0:
try:
traceLog = "Model Location:"+str(self.modelLocation)+"\n"
nBadEx = 0
# Determine Signature and non-Signature descriptor names
cinfonyDesc, clabDesc, signatureHeight, bbrcDesc, signDesc = descUtilities.getDescTypes(descList)
# Signatures
if "sign" in DescMethodsAvailable and signatureHeight:
traceLog += "Calculating signatures...\n"
print "Calculating signatures...."
preCalcData = dataUtilities.DataTable(self.preDefSignatureFile)
startHeight = 0 # Not used desc ignored in model prediction
endHeight = signatureHeight
self.smilesData = getSignatures.getSignatures(self.smilesData, startHeight, endHeight, preCalcData)
# C-Lab desc
if "clab" in DescMethodsAvailable and clabDesc:
traceLog += "Calculating C-Lab...\n"
print "Calculating C-Lab desc...."
self.smilesData = ClabUtilities.appendCLabDesc(clabDesc, self.smilesData)
# Cinfony
if cinfonyDesc:
traceLog += "Calculating Cinfony...\n"
print "Calculating Cinfony desc..."
self.smilesData = getCinfonyDesc.getCinfonyDescResults(self.smilesData, cinfonyDesc, radius = 5)
# bbrcDesc
if "bbrc" in DescMethodsAvailable and bbrcDesc:
traceLog += "Calculating BBRC...\n"
print "Calculating BBRC desc..."
self.smilesData = getBBRCDesc.getBBRCDescResult(self.smilesData, algo = "FTM", minSupPar = 1, descList = bbrcDesc)
# Detect if the descripts calaculation or something else went wrong!
for ex in self.smilesData:
if sum([ex[attr].isSpecial() for attr in self.smilesData.domain.attributes]) == len(self.smilesData.domain.attributes):
nBadEx +=1
if nBadEx:
traceLog += "WARNING: Desc. Calculation: From the "+str(len(self.smilesData))+" compounds, "+str(nBadEx)+" could not be calculated!\n"
print "WARNING: Desc. Calculation: From the "+str(len(self.smilesData))+" compounds, "+str(nBadEx)+" could not be calculated!"
print "WARNING: Tying again..."
self.smilesData = dataUtilities.DataTable(savedSmilesData)
nTry -= 1
else:
nTry = 0
except Exception, e:
errorDesc = "Error Calculating Descriptors:;"+traceLog+str(e)+";"
nTry -= 1
def getDesc(trainDataFile):
# Read the SAR for which to calculate descriptors
sarData = dataUtilities.DataTable(trainDataFile)
# Get names of RDK descriptors
rdkDescs = getCinfonyDesc.getAvailableDescs("rdk")
# Calculate the descriptors
trainData = getCinfonyDesc.getCinfonyDescResults(sarData, rdkDescs)
# Deselect the SMILES attribute
attrList = ["SMILES"]
trainData = dataUtilities.attributeDeselectionData(trainData, attrList)
# Save the trainData set
trainData.save("trainData.tab")
return trainData
def __retrieve(self,descList):
self.error(0)
self.warning(0)
resultsData = None
if not self.data:
self.warning("Missing input data!")
self.send("Examples",None)
return
else:
progressSteps = 5
progress1 = QProgressDialog("Calculating selected descriptors with Cinfony", "Cancel", 0, progressSteps , None, Qt.Dialog )
progress1.setWindowModality(Qt.WindowModal)
progress1.setMinimumDuration(0)
progress1.forceShow()
progress1.setValue(1)
time.sleep(0.1)
progress1.setValue(2)
try:
resultsData = getCinfonyDesc.getCinfonyDescResults(self.data , descList)
progress1.setValue(3)
except:
typeEx, val, traceback = sys.exc_info()
progress1.close()
self.error("Error calculating the descriptors with Cinfony.\n")
print typeEx
print "\t",val
self.send("Examples",None)
return
time.sleep(0.1)
progress1.setValue(4)
time.sleep(0.1)
progress1.setValue(5)
progress1.close()
if resultsData:
self.send("Examples",resultsData)
else:
self.warning("Nothing retrieved from Cinfony.")
self.send("Examples",None)
def getDesc(trainDataFile):
# Read the SAR for which to calculate descriptors
sarData = dataUtilities.DataTable(trainDataFile)
# Get names of RDK descriptors
rdkDescs = getCinfonyDesc.getAvailableDescs("rdk")
# Calculate the descriptors
trainData = getCinfonyDesc.getCinfonyDescResults(sarData, rdkDescs)
# Deselect the SMILES attribute
attrList = [
attr.name for attr in trainData.domain.attributes
if attr.varType == orange.Variable.String
]
trainData = dataUtilities.attributeDeselectionData(trainData, attrList)
# Save the trainData set
trainData.save("trainData.tab")
return trainData
def getAcc(self, callBack=None, algorithm=None, params=None, atts=None, holdout=None):
""" For regression problems, it returns the RMSE and the Q2
For Classification problems, it returns CA and the ConfMat
The return is made in a Dict: {"RMSE":0.2,"Q2":0.1,"CA":0.98,"CM":[[TP, FP],[FN,TN]]}
For the EvalResults not supported for a specific learner/datase, the respective result will be None
if the learner is a dict {"LearnerName":learner, ...} the results will be a dict with results for all Learners and for a consensus
made out of those that were stable
It some error occurred, the respective values in the Dict will be None
parameters:
algorithm - list of feature generation algorithms (set dependent features that have to be calculated inside the crossvalidation)
params - dictionary of parameters
atts - attributes to be removed before learning (e.g. meta etc...)
"""
self.__log("Starting Calculating MLStatistics")
statistics = {}
if not self.__areInputsOK():
return None
if holdout:
self.nExtFolds = 1
if algorithm:
self.__log(" Additional features to be calculated inside of cross-validation")
for i in algorithm:
self.__log(" Algorithm: " + str(i))
for j, v in params.iteritems():
self.__log(" Parameter: " + str(j) + " = " + str(v))
# Set the response type
self.responseType = (
self.data.domain.classVar.varType == orange.VarTypes.Discrete and "Classification" or "Regression"
)
self.__log(" " + str(self.responseType))
# Create the Train and test sets
DataIdxs = None
if holdout:
self.__log("Using hold out evaluation with " + str(holdout) + "*100 % of data for training")
DataIdxs = dataUtilities.SeedDataSampler_holdOut(self.data, holdout)
else:
DataIdxs = dataUtilities.SeedDataSampler(self.data, self.nExtFolds)
# Var for saving each Fols result
optAcc = {}
results = {}
exp_pred = {}
nTrainEx = {}
nTestEx = {}
# Set a dict of learners
MLmethods = {}
if type(self.learner) == dict:
for ml in self.learner:
MLmethods[ml] = self.learner[ml]
else:
MLmethods[self.learner.name] = self.learner
models = {}
rocs = {}
self.__log("Calculating Statistics for MLmethods:")
self.__log(" " + str([x for x in MLmethods]))
# Check data in advance so that, by chance, it will not fail at the last fold!
for foldN in range(self.nExtFolds):
trainData = self.data.select(DataIdxs[foldN], negate=1)
self.__checkTrainData(trainData)
# Optional!!
# Order Learners so that PLS is the first
sortedML = [ml for ml in MLmethods]
if "PLS" in sortedML:
sortedML.remove("PLS")
sortedML.insert(0, "PLS")
stepsDone = 0
nTotalSteps = len(sortedML) * self.nExtFolds
for ml in sortedML:
self.__log(" > " + str(ml) + "...")
try:
# Var for saving each Fols result
results[ml] = []
exp_pred[ml] = []
models[ml] = []
rocs[ml] = []
nTrainEx[ml] = []
nTestEx[ml] = []
optAcc[ml] = []
logTxt = ""
for foldN in range(self.nExtFolds):
if type(self.learner) == dict:
self.paramList = None
trainData = self.data.select(DataIdxs[foldN], negate=1)
orig_len = len(trainData.domain.attributes)
refs = None
methods = [
"rdk_MACCS_keys",
"rdk_topo_fps",
"rdk_morgan_fps",
"rdk_morgan_features_fps",
"rdk_atompair_fps",
]
train_domain = None
# add structural descriptors to the training data (TG)
if algorithm:
for i in range(len(algorithm)):
if algorithm[i] == "structClust":
self.__log("Algorithm " + str(i) + ": " + str(algorithm[i]))
actData = orange.ExampleTable(trainData.domain)
for d in trainData:
# only valid for simboosted qsar paper experiments!?
if d.getclass() == "2":
actData.append(d)
refs = structuralClustering.getReferenceStructures(
actData,
threshold=params["threshold"],
minClusterSize=params["minClusterSize"],
numThreads=2,
)
self.__log(
" found "
+ str(len(refs))
+ " reference structures in "
+ str(len(actData))
+ " active structures"
)
orig_len = orig_len + (len(refs) * len(methods))
trainData_sim = SimBoostedQSAR.getSimDescriptors(refs, trainData, methods)
if i == (len(algorithm) - 1):
trainData = dataUtilities.attributeDeselectionData(trainData_sim, atts)
else:
trainData = dataUtilities.attributeDeselectionData(trainData_sim, [])
elif algorithm[i] == "ECFP":
self.__log("Algorithm " + str(i) + ": " + str(algorithm[i]))
trainData_ecfp = getCinfonyDesc.getCinfonyDescResults(trainData, ["rdk.FingerPrints"])
train_domain = trainData_ecfp.domain
if i == (len(algorithm) - 1):
trainData = dataUtilities.attributeDeselectionData(trainData_ecfp, atts)
else:
trainData = dataUtilities.attributeDeselectionData(trainData_ecfp, [])
else:
self.__log("Algorithm " + str(i) + ": " + str(algorithm[i]))
trainData_structDesc = getStructuralDesc.getStructuralDescResult(
trainData, algorithm[i], params["minsup"]
)
if i == (len(algorithm) - 1):
trainData = dataUtilities.attributeDeselectionData(trainData_structDesc, atts)
else:
trainData = dataUtilities.attributeDeselectionData(trainData_structDesc, [])
# trainData.save("/home/girschic/proj/AZ/ProjDev/train.tab")
testData = self.data.select(DataIdxs[foldN])
# calculate the feature values for the test data (TG)
if algorithm:
for i in range(len(algorithm)):
if algorithm[i] == "structClust":
self.__log(str(algorithm[i]))
testData_sim = SimBoostedQSAR.getSimDescriptors(refs, testData, methods)
if i == (len(algorithm) - 1):
testData = dataUtilities.attributeDeselectionData(testData_sim, atts)
else:
testData = dataUtilities.attributeDeselectionData(testData_sim, [])
elif algorithm[i] == "ECFP":
self.__log(str(algorithm[i]))
# testData_ecfp = orange.ExampleTable(train_domain)
tmp_dat = []
for d in testData:
tmp = getCinfonyDesc.getRdkFPforTestInstance(train_domain, d)
tmp_dat.append(tmp)
testData_ecfp = orange.ExampleTable(tmp_dat[0].domain, tmp_dat)
if i == (len(algorithm) - 1):
# print "removing atts"
testData = dataUtilities.attributeDeselectionData(testData_ecfp, atts)
else:
# print "removing no atts"
testData = dataUtilities.attributeDeselectionData(testData_ecfp, [])
else:
cut_off = orig_len - len(atts)
smarts = trainData.domain.attributes[cut_off:]
self.__log(" Number of structural features added: " + str(len(smarts)))
testData_structDesc = getStructuralDesc.getSMARTSrecalcDesc(testData, smarts)
if i == (len(algorithm) - 1):
testData = dataUtilities.attributeDeselectionData(testData_structDesc, atts)
else:
testData = dataUtilities.attributeDeselectionData(testData_structDesc, [])
# testData.save("/home/girschic/proj/AZ/ProjDev/test.tab")
nTrainEx[ml].append(len(trainData))
nTestEx[ml].append(len(testData))
# Test if trainsets inside optimizer will respect dataSize criterias.
# if not, don't optimize, but still train the model
dontOptimize = False
if self.responseType != "Classification" and (len(trainData) * (1 - 1.0 / self.nInnerFolds) < 20):
dontOptimize = True
else:
tmpDataIdxs = dataUtilities.SeedDataSampler(trainData, self.nInnerFolds)
tmpTrainData = trainData.select(tmpDataIdxs[0], negate=1)
if not self.__checkTrainData(tmpTrainData, False):
dontOptimize = True
if dontOptimize:
logTxt += (
" Fold " + str(foldN) + ": Too few compounds to optimize model hyper-parameters\n"
)
self.__log(logTxt)
if trainData.domain.classVar.varType == orange.VarTypes.Discrete:
res = orngTest.crossValidation(
[MLmethods[ml]],
trainData,
folds=5,
strat=orange.MakeRandomIndices.StratifiedIfPossible,
randomGenerator=random.randint(0, 100),
)
CA = evalUtilities.CA(res)[0]
optAcc[ml].append(CA)
else:
res = orngTest.crossValidation(
[MLmethods[ml]],
trainData,
folds=5,
strat=orange.MakeRandomIndices.StratifiedIfPossible,
randomGenerator=random.randint(0, 100),
)
R2 = evalUtilities.R2(res)[0]
optAcc[ml].append(R2)
else:
runPath = miscUtilities.createScratchDir(
baseDir=AZOC.NFS_SCRATCHDIR, desc="AccWOptParam", seed=id(trainData)
)
# self.__log(" run path:"+str(runPath))
trainData.save(os.path.join(runPath, "trainData.tab"))
tunedPars = paramOptUtilities.getOptParam(
learner=MLmethods[ml],
trainDataFile=os.path.join(runPath, "trainData.tab"),
paramList=self.paramList,
useGrid=False,
verbose=self.verbose,
queueType=self.queueType,
runPath=runPath,
nExtFolds=None,
nFolds=self.nInnerFolds,
logFile=self.logFile,
getTunedPars=True,
)
if not MLmethods[ml] or not MLmethods[ml].optimized:
self.__log(
" WARNING: GETACCWOPTPARAM: The learner " + str(ml) + " was not optimized."
)
self.__log(" It will be ignored")
# self.__log(" It will be set to default parameters")
self.__log(" DEBUG can be done in: " + runPath)
# Set learner back to default
# MLmethods[ml] = MLmethods[ml].__class__()
raise Exception("The learner " + str(ml) + " was not optimized.")
else:
if trainData.domain.classVar.varType == orange.VarTypes.Discrete:
optAcc[ml].append(tunedPars[0])
else:
res = orngTest.crossValidation(
[MLmethods[ml]],
trainData,
folds=5,
strat=orange.MakeRandomIndices.StratifiedIfPossible,
randomGenerator=random.randint(0, 100),
)
R2 = evalUtilities.R2(res)[0]
optAcc[ml].append(R2)
miscUtilities.removeDir(runPath)
# Train the model
model = MLmethods[ml](trainData)
models[ml].append(model)
# Test the model
if self.responseType == "Classification":
results[ml].append(
(
evalUtilities.getClassificationAccuracy(testData, model),
evalUtilities.getConfMat(testData, model),
)
)
roc = self.aroc(testData, [model])
rocs[ml].append(roc)
else:
local_exp_pred = []
for ex in testData:
local_exp_pred.append((ex.getclass(), model(ex)))
results[ml].append(
(evalUtilities.calcRMSE(local_exp_pred), evalUtilities.calcRsqrt(local_exp_pred))
)
# Save the experimental value and correspondent predicted value
exp_pred[ml] += local_exp_pred
if callBack:
stepsDone += 1
if not callBack((100 * stepsDone) / nTotalSteps):
return None
res = self.createStatObj(
results[ml],
exp_pred[ml],
nTrainEx[ml],
nTestEx[ml],
self.responseType,
self.nExtFolds,
logTxt,
rocs[ml],
)
if self.verbose > 0:
print "UnbiasedAccuracyGetter!Results " + ml + ":\n"
pprint(res)
if not res:
raise Exception("No results available!")
statistics[ml] = copy.deepcopy(res)
self.__writeResults(statistics)
self.__log(" OK")
except:
print "Unexpected error:",
print sys.exc_info()[0]
print sys.exc_info()[1]
self.__log(" Learner " + str(ml) + " failed to create/optimize the model!")
res = self.createStatObj(
results[ml],
exp_pred[ml],
nTrainEx[ml],
nTestEx[ml],
self.responseType,
self.nExtFolds,
logTxt,
rocs[ml],
)
statistics[ml] = copy.deepcopy(res)
self.__writeResults(statistics)
if not statistics or len(statistics) < 1:
self.__log("ERROR: No statistics to return!")
return None
elif len(statistics) > 1:
# We still need to build a consensus model out of the stable models
# ONLY if there are more that one model stable!
# When only one or no stable models, build a consensus based on all models
consensusMLs = {}
for modelName in statistics:
StabilityValue = statistics[modelName]["StabilityValue"]
if StabilityValue is not None and statistics[modelName]["stable"]:
consensusMLs[modelName] = copy.deepcopy(statistics[modelName])
self.__log(
"Found " + str(len(consensusMLs)) + " stable MLmethods out of " + str(len(statistics)) + " MLmethods."
)
if len(consensusMLs) <= 1: # we need more models to build a consensus!
consensusMLs = {}
for modelName in statistics:
consensusMLs[modelName] = copy.deepcopy(statistics[modelName])
if len(consensusMLs) >= 2:
# Var for saving each Fols result
Cresults = []
Cexp_pred = []
CnTrainEx = []
CnTestEx = []
self.__log(
"Calculating the statistics for a Consensus model based on " + str([ml for ml in consensusMLs])
)
for foldN in range(self.nExtFolds):
if self.responseType == "Classification":
CLASS0 = str(self.data.domain.classVar.values[0])
CLASS1 = str(self.data.domain.classVar.values[1])
exprTest0 = "(0"
for ml in consensusMLs:
exprTest0 += "+( " + ml + " == " + CLASS0 + " )*" + str(optAcc[ml][foldN]) + " "
exprTest0 += ")/IF0(sum([False"
for ml in consensusMLs:
exprTest0 += ", " + ml + " == " + CLASS0 + " "
exprTest0 += "]),1)"
exprTest1 = exprTest0.replace(CLASS0, CLASS1)
expression = [exprTest0 + " >= " + exprTest1 + " -> " + CLASS0, " -> " + CLASS1]
else:
Q2sum = sum([optAcc[ml][foldN] for ml in consensusMLs])
expression = "(1 / " + str(Q2sum) + ") * (0"
for ml in consensusMLs:
expression += " + " + str(optAcc[ml][foldN]) + " * " + ml + " "
expression += ")"
testData = self.data.select(DataIdxs[foldN])
CnTestEx.append(len(testData))
consensusClassifiers = {}
for learnerName in consensusMLs:
consensusClassifiers[learnerName] = models[learnerName][foldN]
model = AZorngConsensus.ConsensusClassifier(classifiers=consensusClassifiers, expression=expression)
CnTrainEx.append(model.NTrainEx)
# Test the model
if self.responseType == "Classification":
Cresults.append(
(
evalUtilities.getClassificationAccuracy(testData, model),
evalUtilities.getConfMat(testData, model),
)
)
else:
local_exp_pred = []
for ex in testData:
local_exp_pred.append((ex.getclass(), model(ex)))
Cresults.append(
(evalUtilities.calcRMSE(local_exp_pred), evalUtilities.calcRsqrt(local_exp_pred))
)
# Save the experimental value and correspondent predicted value
Cexp_pred += local_exp_pred
res = self.createStatObj(Cresults, Cexp_pred, CnTrainEx, CnTestEx, self.responseType, self.nExtFolds)
statistics["Consensus"] = copy.deepcopy(res)
statistics["Consensus"]["IndividualStatistics"] = copy.deepcopy(consensusMLs)
self.__writeResults(statistics)
self.__log("Returned multiple ML methods statistics.")
return statistics
# By default return the only existing statistics!
self.__writeResults(statistics)
self.__log("Returned only one ML method statistics.")
return statistics[statistics.keys()[0]]
def getDescriptors(self, smiles):
self.getSmilesData(smiles)
# Calculate descriptors defined in the model files
descList = self.model.varNames
savedSmilesData = dataUtilities.DataTable(self.smilesData)
#Try 3 time to get All compounds descriptors
nTry = 3
errorDesc = ""
while nTry > 0:
try:
#if True:
traceLog = "Model Location:" + str(self.modelLocation) + "\n"
nBadEx = 0
# Determine Signature and non-Signature descriptor names
cinfonyDesc, clabDesc, signatureHeight, bbrcDesc, signDesc = descUtilities.getDescTypes(
descList)
# Signatures
if "sign" in DescMethodsAvailable and signatureHeight:
traceLog += "Calculating signatures...\n"
print "Calculating signatures...."
preCalcData = dataUtilities.DataTable(
self.preDefSignatureFile)
startHeight = 0 # Not used desc ignored in model prediction
endHeight = signatureHeight
self.smilesData = getSignatures.getSignatures(
self.smilesData, startHeight, endHeight, preCalcData)
# C-Lab desc
if "clab" in DescMethodsAvailable and clabDesc:
traceLog += "Calculating C-Lab...\n"
print "Calculating C-Lab desc...."
self.smilesData = ClabUtilities.appendCLabDesc(
clabDesc, self.smilesData)
# Cinfony
if cinfonyDesc:
traceLog += "Calculating Cinfony...\n"
print "Calculating Cinfony desc..."
self.smilesData = getCinfonyDesc.getCinfonyDescResults(
self.smilesData, cinfonyDesc, radius=5)
# bbrcDesc
if "bbrc" in DescMethodsAvailable and bbrcDesc:
traceLog += "Calculating BBRC...\n"
print "Calculating BBRC desc..."
self.smilesData = getBBRCDesc.getBBRCDescResult(
self.smilesData,
algo="FTM",
minSupPar=1,
descList=bbrcDesc)
# Detect if the descripts calaculation or something else went wrong!
for ex in self.smilesData:
if sum([
ex[attr].isSpecial()
for attr in self.smilesData.domain.attributes
]) == len(self.smilesData.domain.attributes):
nBadEx += 1
if nBadEx:
traceLog += "WARNING: Desc. Calculation: From the " + str(
len(self.smilesData)) + " compounds, " + str(
nBadEx) + " could not be calculated!\n"
print "WARNING: Desc. Calculation: From the " + str(
len(self.smilesData)) + " compounds, " + str(
nBadEx) + " could not be calculated!"
print "WARNING: Tying again..."
self.smilesData = dataUtilities.DataTable(savedSmilesData)
nTry -= 1
else:
nTry = 0
#else:
except Exception, e:
errorDesc = "Error Calculating Descriptors:;" + traceLog + str(
e) + ";"
nTry -= 1
def parseToFile(assay, data):
descList = getCinfonyDesc.getAvailableDescs("rdkPhysChem")
print descList
data = getCinfonyDesc.getCinfonyDescResults(data, descList)
data.save(assay + "AZOdesc.txt")
