I have enumerated a large set of carbocations all of the formula C10H17+, all of course with differing structures. I know there are many different approaches of computing similarity between molecules, however most work best for molecules with differing formulas. I was wondering if anyone knew what the best method would be to compute similarity of different molecules of the same formula. I am thinking of using some sort of graph based method, but I wanted some advice/guidance on what people may think would be the optimal approach if possible.
I am working on a paper in which I am looking to define some sort of pathway space for the formation of terpenes starting from their carbocation precursors. Eventually I want to build a model that will predict which molecules are most likely to be the next intermediate in a cyclisation reaction, given a certain carbocation as input. I want to start by computing the similarity between the carbocations in some way.