Trying to make reactant and product be more equivalent in double ended method.

The reactant geometry was being stored as self.geometry and the product was pGeom.
Now the reactant is rGeom and the product is pGeom.
Hopefully this clarifies things without breaking anything.

I also tried changing their uniqueIDs. However, some mol files have already been written
by this point. I don't *thing* this commit should break anything, but there may be fragile
things I'm not thinking of.