1. A method for generating theoretical mass spectral fragmentation patterns of a chemical structure comprising: (a) obtaining a description of a chemical structure; (b) generating, from the description, a list of chemical structure information; (c) inputting the list of chemical structure information from step (b) into a tree generator, wherein the tree generator executes computer executable instructions to organize the list in a binary tree data structure; and (d) inputting the binary tree data structure from step (c) into a tree fragmenter, wherein the tree fragmenter executes computer executable instructions to apply predetermined breaking rules to nodes in the binary tree data structure to identify theoretical mass spectral fragmentation patterns of the chemical structure.