build_a_molecule_ideas

class Molecule(object):

    def __init__(self,name=None,smiles=None):
        self.name = name # molecule name
        self.atomlist = someParserGoesHere(smiles) # list of atoms, perhaps list of atom objects???
        self.structure = someParserGoesHere(smiles) # 'structure' attribute should be a 2D connectivity matrix
        self.functionalgroups = ...

    def determineFunctionalGroups(self):
        # Figure out how to get functional groups for visual highlighting.

    def mutateMethod(self,mutate_instruction):
        # some function that adds or removes atoms to the molecule
        # based on some defined syntax, e.g. "add Carbon to C7"

class Atom(object): # or should it be Atom(Molecule), a subclass

    def __init__(self,atomtype=None):
        self.atomtype = atomtype
        # For the variables below I would have some dictionary/function to give these values based on atomtype
        self.mass = massdict['atomtype']
        self.atomicnum = atomicnum...
        self.charge = charge...
        self.numbonds = numbonds... # can be checked to make sure valence is correct

    def printAttributes(self):
        print "Atomtype: %s" % self.atomtype
        print "Mass: %f" % self.mass
        # yadda yadda yadda

class Bond(Molecule):
    pass

class FunctionalGroup(Molecule):
    pass