The atomic, molecular and reaction signature coding. A) The process for computing the molecular signature for a compound C is illustrated for 6-aminohexanate. The process starts by computing the atomic signature for each atom. In the given example, the atomic signature for the carbon in the carboxylic group is computed up to height h = 2. At height h = 0 (blue), the molecular graph rooted at the atom is given by the atom itself; at height h = 1 (green) a canonical representation of the root atom and its first atomic neighbors are given; the process continues similarly for heights h = 2 (orange) and higher until the diameter of the graph is reached. Atomic signatures are collected for all atoms and sorted in order to provide the molecular signature, for instance the molecular signature 1σ(C) of height h = 1 is given at the left; B) The coding of reactions signatures is illustrated for the 6-aminohexanoate hydrolase (EC 184.108.40.206). The reaction signature contains the net difference between the products and the substrates. In the figure, the reaction signature 1σ(R) was computed for height h = 1; C) Illustration of how signatures of reactions provide a way to measure their chemical similarity. For example, the previous reaction (EC 220.127.116.11) has the same signature at height h = 1 than 4-(γ-glutamylamino)butanoate amidohydrolase (EC 18.104.22.168). However, both signatures differ at height h = 2, having in this case a Tanimoto similarity of 2s(R1, R2) = 0.81 (see Equation 14 in Methods).