Fig. 5

ReactionCode encoding algorithm: Once all atoms and bonds are encoded, all encoded atoms present in the reaction center (depth = 0) are reverse sorted. If two or more atoms have the same code, the conflict solver algorithm is started. The conflict algorithm will make a tree of the connected atom (see Additional file 1: Figure S2) and compare the atom codes and the bond codes of the atom present in the next layer using a BFS algorithm. The algorithm iterates until the conflicts are solved and a proper order can be set up. Then, the connections between the atoms in the current layer are made. Then, all the atoms present in the depth n + 1 (if any), which will be all atoms connected with those in the reaction center in this situation, are reverse sorted. If there are any conflicts, they are first solved by comparing the position of the connected atoms in the previous layer, then using the connected bonds, the atom properties (stereochemistry, charge and isotopy) and finally in the next layer(s) if the conflict cannot be solved. We iterate this process until all layers are processed