The SMARTS in the resulting hierarchy mapped to Sage SMARTS with 100% accuracy, but only if the search space was large enough. For the single molecule hierarchies, we found that all hierarchies were 100% accurate across all search spaces considered. This means that the method was able to discriminate all chemical environments in each individual molecule. The accuracy drops to 99.4% when 49 molecules were used to build the hierarchy using the smallest search space possible, a bit depth of 1 and a graph depth of 0. With 49 molecules, it is more difficult to distinguish the chemical environments, and a larger search space is needed. After increasing the graph depth of 1, a 100% accuracy was recovered for the 49 molecules. The resulting SMARTS of the 100% accu- rate molecule corresponding to b = 1 d = 1 is listed in SI Sec. 3.2. This result correlates with the Sage SMARTS patterns since some of them have a graph depth of 1. We needed to increase our search space to include the additional graph depth because the primitives at the graph depth of 0 were not able to distinguish these more complex chemical environments.