The OpenMM toolkit was used to initially load the PDB topology since it specializes in loading biopolymer systems with support for general polymer systems if explicit CONECT records are given. The RDKit toolkit was used to perform the substructure pattern match from the template to the polymer and subsequently copy chemical information. As part of the substructure pattern match, input monomer templates are first aromaticized with the MDL aromaticity model before performing queries. Although the templates and final PDB are only allowed to be kekulized, matching with an aromaticity model helps to avoid cases where kekulized representations of identical aromatic bonds may disagree in their matching.