ChemPer has proven to be capable of automatically generating relatively simple SMIRKS patterns which identify chemical differences between clustered fragments. It is successful at extracting and combining decorators for multiple fragments into one pattern. Each step in SMIRKS generation is separated into its own module (Section 3). We have shown some early success here by replicating smirnoff99Frosst parameters for AlkEthOH. We also automatically created SMIRKS patterns which replicated the typing in a common protein force field. The scripts required for both of these tests are available in the Supporting Information.