Algorithms were developed to allow for molecular-level reaction pathways to be described through a series of topological "site neighborhood"-based cases. These mechanism-informed pathway-level models capture mechanistic knowledge that would otherwise have been lost in a traditional pathway model with far fewer species than a mechanistic model would entail. Protonated cyclopropane (PCP) isomerization and beta-scission cracking are explored in detail to demonstrate the capture of the different energies of carbenium ion transitions.