Abstract: Reaction transforms described herein contain syntactically separate the matching and processing functions of a transform. Using its matching function, a transform selects specific building blocks and reacting sites from a set of building blocks. The transform selects only those building blocks and reacting sites that match a generic reactant substructure presented in the transform and possibly any other requirements and constraints present in the matching function. The transform then processes the selected building blocks by manipulating bonds and arrangements of atoms as required by the processing function specified in the transform. The processing function allows non-reaction center atoms and bonds to be processed independent from their structural context and specific chemical and physical properties. The processing function still preserves intra- and intermolecular character of a transformation.

Abstract: Computational tools automatically suggest/generate diverse reaction sets for particular precursors, classes of precursors, or different reaction chemistries. This is accomplished by automatically generating a group of reaction chemistries for a particular precursor or class of precursors. Some of the reactions and/or products may be produced without reliance on reactions and products reported in available references.

Abstract: Reaction steps are organized as belonging to particular reaction protocols within a database. Each reaction may represent a discrete step in a multi-step protocol for making a final product from a starting reactant. To populate the database, a system receives information separately from a plurality of references (e.g., literature articles, patent publications, etc.). Such information typically includes descriptions of reaction steps presented in the references (e.g., detailed recipes for performing the reaction steps). Alternatively, or in addition, the methodology includes identifying at least one protocol specified in the reference, which protocol comprises two or more reaction steps, and then specifying that the two or more reaction steps belong to the protocol.