Balsa: A Compact Line Notation Based on SMILES

Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses these problems. A formal, machine- readable grammar defines Balsa’s syntax. Semantics are described at three levels of resolution: constitution; configuration; and conformation. To estimate the compatibility of Balsa strings with SMILES software, all differences between the two languages were enumerated. To the extent that SMILES documentation is unambiguous, every difference was consistent with Balsa being a language subset.