The Chemal algorithm processes ESRA’s stochastic output by aligning molecular graphs across sequential time steps. Chemal solves the graph isomorphism problem for each frame, tracking which bonds break or form. It uses a dynamic programming routine that compares adjacency matrices, weighted by atomic species and partial charges. Without Chemal, ESRA would produce unlabeled trajectories; with it, one obtains a “reaction network” of elementary steps.
This number often correlates with specific file labels (e.g., tina-tina-131-imgsrcru.pdf esra model chemal gegg 131