Grammar-driven SMILES standardization with <i>TokenSMILES</i>.

ABSTRACT: The redundancy of SMILES notation, where multiple strings can describe the same molecule, remains a challenge in computational chemistry and cheminformatics. To mitigate this issue, we introduce TokenSMILES, a grammatical framework that standardizes SMILES into structured sentences composed of context-free words. By applying five syntactic constraints (including branch limitations, balanced parentheses, and aromaticity exclusion), TokenSMILES minimizes redundant SMILES enumerations for alkanes while maintaining valence and octet compliance through semantic parsing rules. TokenSMILES does not replace SMILES but rather formalizes its syntax into a standardized, machine-interpretable form. This grammatical structure enables controlled generatio

SUBMITTER: Gonzalez-Ortiz LA 

PROVIDER: S-EPMC12653016 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature