In this paper, we introduce ChemPer, a new tool for automatically determining SMIRKS patterns. Previous research has shown that generating SMIRKS patterns matching the chemical complexity of human derived chemical perception is a very difficult problem . Therefore, in this work we will focus on SMIRKS generation assuming we already know which parameters we wish to assign to a set of molecules. That is the input for ChemPer modules are molecular fragments already clustered by which parameter they should be assigned. We validate these algorithms in two ways. First, we assign parameters to AlkEthOH -a set of alkanes, ethers, and alcohols -with a reference force field and generate new SMIRKS to match that clustering. Second, we type a set of polypeptides with Amber99SB-ILDN and attempt to generate SMIRKS patterns to recover these typing rules. These SMIRKS patterns could be used to create the first protein force field in the SMIRNOFF format. We conclude with a discussion of other possible applications and areas for potential improvement in the future. ChemPer is open source and available to the public at .