Chemical reactions definitely require more descriptors due to the possible existence of multiple reaction branches. The properties such as activation energy and reaction enthalpy may be appropriate, but are impractical due to time-consuming quantum chemical calculations. The reaction fingerprints, which are calculated by the difference of the molecular fingerprints of reactants and products, have been successfully applied in reaction classification and similarity assessment. In the same spirit, the molecular similarity based on molecular fingerprints is used in this work as a reaction descriptor to represent different branches from a reaction. Molecular fingerprints are bit string representations of chemical structures originally designed for chemical database substructure searching and analysis. The Morgan molecular fingerprints, which are widely utilized as binary features for the quantification of structural similarity of chemical compounds in two dimension, are employed to calculate the molecular similarity to describe H-abstraction reactions at different sites. The cosine similarity is used in this work and calculated by 43