def test_ftm(self):
"""Test if ftm is running properly"""
result = getBBRCDesc.getBBRCDescResult(self.data,"FTM", 6)
expected_atts = 31
expected_data_length = 32
self.assertEqual(expected_atts,len(result.domain.attributes))
self.assertEqual(expected_data_length, len(result[0]))
def test_smartsRecalc(self):
"""Test bbrc feature recalculation"""
result = getBBRCDesc.getBBRCDescResult(self.data, "FTM", 6)
smarts = [smrt.name for smrt in result.domain.attributes[len(self.data.domain.attributes):]]
result2 = getBBRCDesc.getSMARTSrecalcDesc(self.data,smarts)
#expected_atts = 3
self.assertEqual(len(result),len(result2))
def test_ftm(self):
"""Test if ftm is running properly"""
result = getBBRCDesc.getBBRCDescResult(self.data, "FTM", 6)
expected_atts = 31
expected_data_length = 32
self.assertEqual(expected_atts, len(result.domain.attributes))
self.assertEqual(expected_data_length, len(result[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:
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 test_bbrc(self):
""" Test if bbrc is running properly """
import bbrc
# the minimum support for BBRC is absolute not relative like for FTM
result = getBBRCDesc.getBBRCDescResult(self.data, "BBRC", 2)
expected_atts = 9
expected_data_length = 10
self.assertEqual(expected_atts,len(result.domain.attributes))
self.assertEqual(expected_data_length, len(result[0]))
def test_bbrc(self):
""" Test if bbrc is running properly """
import bbrc
# the minimum support for BBRC is absolute not relative like for FTM
result = getBBRCDesc.getBBRCDescResult(self.data, "BBRC", 2)
expected_atts = 9
expected_data_length = 10
self.assertEqual(expected_atts, len(result.domain.attributes))
self.assertEqual(expected_data_length, len(result[0]))
def test_smartsRecalc(self):
"""Test bbrc feature recalculation"""
result = getBBRCDesc.getBBRCDescResult(self.data, "FTM", 6)
smarts = [
smrt.name for smrt in
result.domain.attributes[len(self.data.domain.attributes):]
]
result2 = getBBRCDesc.getSMARTSrecalcDesc(self.data, smarts)
#expected_atts = 3
self.assertEqual(len(result), len(result2))
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
