I have a number of chemicals with corresponding data held within a database, how do I go about returning a specific chemical, and its data, via its formula, eg o2.
class SourceNotDefinedException(Exception):
def __init__(self, message):
super(SourceNotDefinedException, self).__init__(message)
class tvorechoObject(object):
"""The class stores a pair of objects, "tv" objects, and "echo" objects. They are accessed
simply by doing .tv, or .echo. If it does not exist, it will fall back to the other variable.
If neither are present, it returns None."""
def __init__(self, echo=None, tv=None):
self.tv = tv
self.echo = echo
def __repr__(self):
return str({"echo": self.echo, "tv": self.tv}) # Returns the respective strings
def __getattribute__(self, item):
"""Altered __getattribute__() function to return the alternative of .echo / .tv if the requested
attribute is None."""
if item in ["echo", "tv"]:
if object.__getattribute__(self,"echo") is None: # Echo data not present
return object.__getattribute__(self,"tv") # Select TV data
elif object.__getattribute__(self,"tv") is None: # TV data not present
return object.__getattribute__(self,"echo") # Select Echo data
else:
return object.__getattribute__(self,item) # Return all data
else:
return object.__getattribute__(self,item) # Return all data
class Chemical(object):
def __init__(self, inputLine, sourceType=None):
self.chemicalName = TVorEchoObject()
self.mass = TVorEchoObject()
self.charge = TVorEchoObject()
self.readIn(inputLine, sourceType=sourceType)
def readIn(self, inputLine, sourceType=None):
if sourceType.lower() == "echo": # Parsed chemical line for Echo format
chemicalName = inputLine.split(":")[0].strip()
mass = inputLine.split(":")[1].split(";")[0].strip()
charge = inputLine.split(";")[1].split("]")[0].strip()
# Store the objects
self.chemicalName.echo = chemicalName
self.mass.echo = mass
self.charge.echo = charge
elif sourceType.lower() == "tv": # Parsed chemical line for TV format
chemicalName = inputLine.split(":")[0].strip()
charge = inputLine.split(":")[1].split(";")[0].strip()
mass = inputLine.split(";")[1].split("&")[0].strip()
# Store the objects
self.chemicalName.tv = chemicalName
self.charge.tv = charge
self.mass.tv = molecularWeight
else:
raise SourceNotDefinedException(sourceType + " is not a valid `sourceType`") # Otherwise print
def toDict(self, priority="echo"):
"""Returns a dictionary of all the variables, in the form {"mass":<>, "charge":<>, ...}.
Design used is to be passed into the Echo and TV style line format statements."""
if priority in ["echo", "tv"]:
# Creating the dictionary by a large, to avoid repeated text
return dict([(attributeName, self.__getattribute__(attributeName).__getattribute__(priority))
for attributeName in ["chemicalName", "mass", "charge"]])
else:
raise SourceNotDefinedException("{0} source type not recognised.".format(priority)) # Otherwise print
from ParseClasses import Chemical
allChemical = []
chemicalFiles = ("/home/temp.txt")
for fileName in chemicalFiles:
with open(fileName) as sourceFile:
for line in sourceFile:
allChemical.append(Chemical(line, sourceType=sourceType))
for chemical in allChemical:
print chemical.chemicalName #Prints all chemicals and their data in list format
for chemical in allChemical(["o2"]):
print chemical.chemicalName
outputs the following error which I have tried to remedy with no luck; TypeError: 'list' object is not callable
Try this function:
def chemByString(chemName,chemicals,priority="echo"):
for chemical in chemicals:
chemDict = chemical.toDict(priority)
if chemDict["chemicalName"] == chemName
return chemical
return None
This function is using the toDict() method found in the Chemical class. The code you pasted from the Chemical class explains that this method returns a dictionary from the chemical object:
def toDict(self, priority="echo"):
"""Returns a dictionary of all the variables, in the form {"mass":<>, "charge":<>, ...}.
Design used is to be passed into the Echo and TV style line format statements."""
if priority in ["echo", "tv"]:
# Creating the dictionary by a large, to avoid repeated text
return dict([(attributeName, self.__getattribute__(attributeName).__getattribute__(priority))
for attributeName in ["chemicalName", "mass", "charge"]])
else:
raise SourceNotDefinedException("{0} source type not recognised.".format(priority)) # Otherwise print
This dictionary looks like this:
"chemicalName" : <the chemical name>
"mass" : <the mass>
"charge" : <the charge>
What the function I created above does is iterate through all of the chemicals in the list, finds the first one with a name equal to "o2", and returns that chemical. Here's how to use it:
chemByString("o2",allChemicals).chemicalName
If the above does not work, may want to try using the alternative priority ("tv"), though I'm unsure if this will have any effect:
chemByString("o2",allChemicals,"tv").chemicalName
If the chemical isn't found, the function returns None:
chemByString("myPretendChemical",allChemicals).chemicalName