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 __initListBox(self):
## Get available descriptors from Cinfony and show progress bar.
progressSteps = 3
progress1 = QProgressDialog("Retrieving available descriptors from 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:
availableDescriptors = getCinfonyDesc.getAvailableDescs()
except:
typeEx, val, traceback = sys.exc_info()
progress1.close()
#self.updateInfo()
self.error("Error retrieving descriptors from Cinfony.\n")
print typeEx
print "\t",val
return
progress1.setValue(3)
progress1.close()
# Create a sorted list of descriptors available in Cinfony
self.Descriptors.setInputItems(availableDescriptors)
#toolkitsEnabled
if getCinfonyDesc.toolkitsEnabled:
self.info.setText("Toolkits available for retrieving descriptors: "+ str(getCinfonyDesc.toolkitsEnabled)[1:-1].replace("'",""))
else:
self.error("No available toolkits for retrieving descriptors!")
self.info.setText("Cinfony returned no available scripts!")
def getDescTypes(descList):
clabDescList = []
cinfonyDescList = []
bbrcDesc = []
signDesc = []
signatureHeight = None
cinfonyDescs = getCinfonyDesc.getAvailableDescs()
cinfonyTags = [tk["tag"] for tk in getCinfonyDesc.toolkitsDef.values()]
for desc in descList:
if desc in AZOC.SMILESNAMES:
continue
# Cinfony
if desc in cinfonyDescs or sum([tag in desc for tag in cinfonyTags]):
cinfonyDescList.append(desc)
# None signature CLab
elif "clab" in DescMethodsAvailable and string.find(desc, "[") != 0:
if desc == "SMILES" or desc == "ID":
print "Warning"
print "The model was built with SMILES or IDs!!"
else:
clabDescList.append(desc)
# BBRCDesc
elif "bbrc" in DescMethodsAvailable and desc[0] == "[" and desc[
1] == "#" and "&" in desc:
bbrcDesc.append(desc)
# Signature descriptor by exclusion
elif "sign" in DescMethodsAvailable: # else!!
newSignatureHeight = getSignatures.getSignatureHeight(desc)
signDesc.append(desc)
if newSignatureHeight > signatureHeight:
signatureHeight = newSignatureHeight
return cinfonyDescList, clabDescList, signatureHeight, bbrcDesc, signDesc
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 getDescTypes(descList):
clabDescList = []
cinfonyDescList = []
bbrcDesc = []
signDesc = []
signatureHeight = None
cinfonyDescs = getCinfonyDesc.getAvailableDescs()
cinfonyTags = [tk["tag"] for tk in getCinfonyDesc.toolkitsDef.values()]
for desc in descList:
if desc in AZOC.SMILESNAMES:
continue
# Cinfony
if desc in cinfonyDescs or sum([tag in desc for tag in cinfonyTags]):
cinfonyDescList.append(desc)
# None signature CLab
elif "clab" in DescMethodsAvailable and string.find(desc, "[") != 0:
if desc == "SMILES" or desc == "ID":
print "Warning"
print "The model was built with SMILES or IDs!!"
else:
clabDescList.append(desc)
# BBRCDesc
elif "bbrc" in DescMethodsAvailable and desc[0] == "[" and desc[1] == "#" and "&" in desc:
bbrcDesc.append(desc)
# Signature descriptor by exclusion
elif "sign" in DescMethodsAvailable: # else!!
newSignatureHeight = getSignatures.getSignatureHeight(desc)
signDesc.append(desc)
if newSignatureHeight > signatureHeight: signatureHeight = newSignatureHeight
return cinfonyDescList, clabDescList, signatureHeight, bbrcDesc, signDesc
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 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
import os
from AZutilities import dataUtilities
from AZutilities import getCinfonyDesc
import Orange
import orange
#fileName = "XEN025dragonNewHeaderResp.txt"
fileName = "LiuJCIM2015dragonNewHeaderResp.txt"
path, ext = os.path.splitext(fileName)
outFileName = path + "RDKbulk" + ext
data = dataUtilities.DataTable(fileName)
descList = getCinfonyDesc.getAvailableDescs("rdkPhysChem")
newData = getCinfonyDesc.getRdkDescResult(data, descList)
#descList = getCinfonyDesc.getAvailableDescs("rdk")
#newData = getCinfonyDesc.getRdkDescResult(data, descList, radius = 3)
newData.save(outFileName)
def parseToFile(assay, data):
descList = getCinfonyDesc.getAvailableDescs("rdkPhysChem")
print descList
data = getCinfonyDesc.getCinfonyDescResults(data, descList)
data.save(assay + "AZOdesc.txt")
