Genetic Algorithms

I’ve been working on implementing crossover of two molecules. I’ve gotten a rudimentary crossover implementation (it uses Fragmenter2 to generate all the possible fragments of each of the parent molecules, picks two random, and joins them at two random atoms) that will probably need to be improved, but it’s good for now.

I’m getting a bunch of errors in my code when I try to run several generations at once, so the next thing for me to do is resolve these NullPointerExceptions. I think it might be caused by creating invalid molecule objects with some of the new methods in the AtomUtils class, or some of the changes I made to Mutations. I hope to have this fixed soon.