def detetminePrimaryAmine(self, nitrogenIndex):
""" Return primary amine Molecule object with proper ring classification, if it exists on a ring
Return false if nitrogen is not a primary amine
nitrogenIndex (int) : The index of the nitrogen in the smiles code to be analyzed for being a primary amine
"""
nitrogenBonds = self.bondData[
nitrogenIndex] # Get bonds connected to nitrogen
if (len(nitrogenBonds) == 1 # Primary amines have one bond
and not self.BOND_REGEX.findall(
nitrogenBonds[0].symbol) # That must be a single bond
): # Otherwise, nitrogen is not a primary amine
bondedIndex = nitrogenBonds[0].index
primaryAmine = Molecule(
"RN", "PrimaryAmine") # Create primary amine Molecule object
primaryAmine.atomData[
0].index = bondedIndex # Set the R group index to the smiles bonded nitrogen index
primaryAmine.atomData[
1].index = nitrogenIndex # Set the nitrogen index to the smiles code nitrogen index
if bondedIndex in self.AROMATICINDICES: # Add aromatic nomenclature if necessary
primaryAmine.NAME = "AromaticPrimaryAmine"
elif bondedIndex in self.CYCLICINDICES: # Or cyclic nomenclature
primaryAmine.NAME = "CyclicPrimaryAmine"
return primaryAmine # Return the primary amine object if true
return False # Otherwise return false
def determineAlcoholGroups(self, functionalGroups):
""" Appends the functional groups created from alocholic oxygens, with ring classifications, to the functionalGroups list passed in.
functionalGroups (list) : List of Molecule obejects that represent the functional groups of a SMILES code
Notes:
This function looks to see if the alcoholic oxygen is attached within an aromatic, non-aromatic ring strucutres, or no at all
Build upon alochol indices found in the molecule
"""
for index in self.ALCOHOLICINDICES:
alohcolBond = self.bondData[index]
alochol = Molecule("RO", "Alcohol")
alochol.atomData[0].index = alohcolBond[0].index
alochol.atomData[1].index = index
if alohcolBond[0].index in self.AROMATICINDICES:
alochol.NAME = "AromaticAlcohol"
elif alohcolBond[0].index in self.CYCLICINDICES:
alochol.NAME = "CyclicAlcohol"
functionalGroups.append(alochol)
return
