def sendData(self):
"""Sends out data.
"""
if self.varA and self.varB:
etAB = dataUtilities.horizontalMerge(self.dataA,self.dataB,self.varA,self.varB)
self.send("Merged Examples A+B", etAB)
etBA = dataUtilities.horizontalMerge(self.dataB,self.dataA,self.varB,self.varA)
self.send("Merged Examples B+A", etBA)
else:
self.send("Merged Examples A+B", None)
self.send("Merged Examples B+A", None)
def getCinfonyDescResults(origData,descList,radius=1):
"""Calculates the cinfony descriptors on origData
maintains the input variables and class
Adds the Cinfony descritors
Returns a new Dataset"""
if not origData or not descList: return None
smilesName = getSMILESAttr(origData)
if not smilesName: return None
#Create a new domain saving original smiles and other attributes
newDomain = orange.Domain([attr for attr in origData.domain if attr is not origData.domain.classVar] + [orange.StringVariable("origSmiles")],origData.domain.classVar)
data = dataUtilities.DataTable(newDomain, origData)
# Standardize SMILES
for ex in data:
ex["origSmiles"] = ex[smilesName].value
#TODO: Call here some method to standardize the attribute smilesName in place having the attr origSmiles as ID
results = []
# Calculate available descriptors
res = getObabelDescResult(data,descList)
if res: results.append(res)
res = getRdkDescResult(data,descList,radius)
if res: results.append(res)
res = getWebelDescResult(data,descList)
if res: results.append(res)
res = getCdkDescResult(data,descList)
if res: results.append(res)
# Convert any nan to a '?'
if len(results):
for res in results:
for ex in res:
for attr in ex.domain:
if ex[attr] != ex[attr]: # Will fail if it is 'nan'
ex[attr] = '?'
# return None if no results at all
if not results:
return None
resData = results[0]
if len(results) > 1:
for res in results[1:]:
resData = dataUtilities.horizontalMerge(resData, res, smilesName, smilesName)
data = dataUtilities.horizontalMerge(data, resData, smilesName, smilesName)
# Revert the SMILES back to it's original state
for ex in data:
ex[smilesName] = ex["origSmiles"]
#Remove the origSmiles attributes
data = dataUtilities.DataTable(orange.Domain([attr for attr in data.domain if attr.name != "origSmiles" and attr is not data.domain.classVar],data.domain.classVar),data)
return data
def getCinfonyDescResults(origData,descList,radius=1):
"""Calculates the cinfony descriptors on origData
maintains the input variables and class
Adds the Cinfony descritors
Returns a new Dataset"""
if not origData or not descList: return None
smilesName = getSMILESAttr(origData)
if not smilesName: return None
#Create a new domain saving original smiles and other attributes
newDomain = orange.Domain([attr for attr in origData.domain if attr is not origData.domain.classVar] + [orange.StringVariable("origSmiles")],origData.domain.classVar)
data = dataUtilities.DataTable(newDomain, origData)
# Standardize SMILES
for ex in data:
ex["origSmiles"] = ex[smilesName].value
#TODO: Create a method in dataUtilities to standardize the attribute smilesName in place having the attr origSmiles as ID
if "AZutilities.extraUtilities" in sys.modules and hasattr(extraUtilities, "StandardizeSMILES"):
# Call a method for standardizing the SMILES in Data.
# The method is expected to change the attribute defined as smiAttr in data object
# +->Data +-> SMILES attribuite name +->Compound Name or attribute to act as an ID"
extraUtilities.StandardizeSMILES(data, smiAttr = smilesName, cName="origSmiles")
results = []
# Calculate available descriptors
res = getObabelDescResult(data,descList)
if res: results.append(res)
res = getRdkDescResult(data,descList,radius)
if res: results.append(res)
res = getWebelDescResult(data,descList)
if res: results.append(res)
res = getCdkDescResult(data,descList)
if res: results.append(res)
# Convert any nan to a '?'
if len(results):
for res in results:
for ex in res:
for attr in ex.domain:
if ex[attr] != ex[attr]: # Will fail if it is 'nan'
ex[attr] = '?'
# return None if no results at all
if not results:
return None
resData = results[0]
if len(results) > 1:
for res in results[1:]:
resData = dataUtilities.horizontalMerge(resData, res, smilesName, smilesName)
data = dataUtilities.horizontalMerge(data, resData, smilesName, smilesName)
# Revert the SMILES back to it's original state
for ex in data:
ex[smilesName] = ex["origSmiles"]
#Remove the origSmiles attributes
data = dataUtilities.DataTable(orange.Domain([attr for attr in data.domain if attr.name != "origSmiles" and attr is not data.domain.classVar],data.domain.classVar),data)
return data
from AZutilities import dataUtilities
#file1 = "XEN025dragonNewHeaderRespRDKbulk.txt"
#file2 = "XEN025SMARTcyp.txt"
file1 = "LiuJCIM2015SMARTcyp.txt"
file2 = "LiuJCIM2015dragonNewHeaderRespRDKbulk.txt"
data1 = dataUtilities.DataTable(file1)
data2 = dataUtilities.DataTable(file2)
#data = dataUtilities.horizontalMerge(data1, data2, "NAME", "MV Number")
#data = dataUtilities.horizontalMerge(data1, data2, "NAME", "MVnumber")
data = dataUtilities.horizontalMerge(data1, data2, "MVnumber", "NAME")
#data.save("XEN025dragonNewHeaderRespRDKbulkSMARTcyp.txt")
data.save("LiuJCIM2015dragonNewHeaderRespRDKbulkSMARTcyp.txt")