When working types have only very generic SMARTS pattern they will match the most populated reference atom type due to our typing scheme and scoring function. The scoring function uses a bipartite graph where the matching is based on the maximum total weight and the weight on each edge is determined by the number of atoms assigned that working and reference type (Section 2.1.1). For this reason, a reference type with the highest population is more likely to be matched with a generic working type. To understand the implications of this, consider the frequency of two of the carbon types in MiniDrugBank, CT and CA. The parm99/parm@Frosst atom type CT is assigned to 2213 atoms, while CA is used for 2097. If we have only one carbon SMARTS string, such as the generic one "[#6]", all carbon atoms in the molecule set will be assigned as "[#6]", and after scoring, the SMARTS pattern will match the reference atom type CT because it leads to the highest total score. In that case, CA (and all other carbon atom types) are not matched to any SMARTS. But, if we discover a new working atom type that matches CT only, such as "[#6X4]", then the generic SMARTS will match CA (Figure ).