{
    "protocol": "The HeadTailAssign (HTA) algorithm quantifies the reactivity of the functional groups of the monomer structure and assigns special characters to those positions in the output SMILES.1. Input a csv file containing the polymer name and either a reaction SMILES or a monomer SMILES. 2. If a reaction SMILES is provided, use HTA to identify the monomer by evaluating Chemical Similarity. 3. Separate molecular entities and calculate fingerprints using RDKFingerprint. 4. Compare fingerprints using Tanimoto Similarity and select the reactant SMILES with the highest similarity score as monomer SMILES. 5. Use the Assigner module to perform classification tasks and tag head and tail atoms. 6. For identifying the polymer class, compare the monomer SMILES with SMARTS of common functional groups. 7. For polyamide, ensure a primary amine and a carboxylic acid or a secondary amide and a heterocycle monomer are present. 8. For polyester, ensure an aliphatic alcohol group and a carboxylic acid group or a heterocycle group and a carboxylic acid group are present. 9. For polyether, ensure an ether group and perform ring-opening. 10. For polyurethane, include one monomer with an alcohol group and another with a cyanate group. 11. Calculate the nucleophilicity index using the STO-3G basis set and Mulliken’s population analysis method. 12. Generate the GAMESS input file by converting the SMILES string into a 3D coordinate file with OpenBabel and geometry optimization. 13. Extract HOMO population data from the GAMESS output file to calculate R_X for each atom. 14. Rank R_X in descending order to identify the functional group with the highest reactivity as the polymerization site. 15. Assign the polymer to its class based on the highest R_X functional group. 16. Use the Get Class routine to obtain the polymerization mechanism. 17. Assign the head and tail atoms in the monomer SMILES according to the defined polymerization rules. 18. Compile the results in csv format, including polymer name, reaction SMILES, assignment results for monomer, polymer class, polymerization mechanism, head, and tail atoms."
}