We have restricted ourselves to just three types of elementary reactions, but similar conclusions can be drawn for other processes using the provided methodology. Our query software has been written with sufficient generality in mind, to quickly query any reactant (with any short-and long-range features), remove leaving groups, build any specified functional group, add/remove bonds at the reactions site, and extract embeddings at the reaction site, in a fully automated manner. The software is open source and the link can be found in the Supplementary Section.