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 by: (i) designating an atom node in a non-ring chain as a root node; (ii) building a tree frame extending from the root node wherein each node in the tree frame corresponds to an atom in the non-ring chain and wherein adjacent atoms in the non-ring chain have a parent—right-child node relationship in the tree frame; and, (iii) generating a left-child subtree for each node in the tree frame; (c) inputting the list of chemical structure information from step (b) into a tree generator, and using the tree generator to execute 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, and using the tree fragmenter to execute 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.