The first part of loading a PDB file into a chemical system in this workflow is to insert bond orders and formal charges, which can be challenging for large polymer topologies. Existing cheminformatics tools such as RDKit's rdDetermineBonds function can guess chemical information from a molecular graph using sets of rules involving ground-state electron config-urations and the total charge of the molecule. However, research into automatic bond-order guessers on large sets of small molecules show that while rule-based algorithms can achieve accurate results for the vast majority of molecules, a small percentage of chemistries tends to evade the bond type assignment algorithm. Even with explicit hydrogen atoms, bondorder guessers can still fail to predict uncommon resonance forms around electron donors and acceptors, such as those seen around N, O and S in Figure . As such, it is recommended that bond order guesser be used with caution, and that their output be verified. This is feasible for small molecules but not for large topologies with thousands of atoms which cannot be manually inspected with certainty; these require other methods to ensure correct chemical information assignment for direct chemical perception. To obtain chemical information for large polymers, we propose the use of monomer information templates whose information is applied throughout a polymer system based on the information available in a PDB file as described in Figure . This approach leverages the repeating nature of polymers by first decomposing a monomer into an element-labeled graph and finding subgraph matches in the polymer. Chemical information is then copied from the repeating subunit into the polymer graph. This approach is preferable to automatic bond order guessers because it allows fine control over and certainty in the final chemical information throughout the polymer system without the need to tediously verify the entire structure. Template-based matching also catches chemically ambiguous chemistries when two or more templates assign different bond orders and formal charges to the same area of the PDB topology. For example, a collection of templates that contain any two of the adjacent moieties in Figure and match to the same repeating subunit in the polymer could be rejected from the loading step, requiring more specific and/or more homogeneous templates.