Jmol SMILES and Jmol SMARTS: specifications and applications.

BACKGROUND: SMILES and SMARTS are two well-defined structure matching languages that have gained wide use in cheminformatics. Jmol is a widely used open-source molecular visualization and analysis tool written in Java and implemented in both Java and JavaScript. Over the past 10 years, from 2007 to 2016, work on Jmol has included the development of dialects of SMILES and SMARTS that incorporate novel aspects that allow new and powerful applications.
RESULTS: The specifications of "Jmol SMILES" and "Jmol SMARTS" are described. The dialects most closely resemble OpenSMILES and OpenSMARTS. Jmol SMILES is a superset of OpenSMILES, allowing a freer format, including whitespace and comments, the addition of "processing directives" that modify the meaning of certain aspects of SMILES processing such as aromaticity and stereochemistry, a more extensive treatment of stereochemistry, and several minor additions. Jmol SMARTS similarly adds these same modifications to OpenSMARTS, but also adds a number of additional "primitives" and elements of syntax tuned to matching 3D molecular structures and selecting their atoms. The result is an expansion of the capabilities of SMILES and SMARTS primarily for use in 3D molecular analysis, allowing a broader range of matching involving any combination of 3D molecular structures, SMILES strings, and SMARTS patterns. While developed specifically for Jmol, these dialects of SMILES and SMARTS are independent of the Jmol application itself.
CONCLUSIONS: Jmol SMILES and Jmol SMARTS add value to standard SMILES and SMARTS. Together they have proven exceptionally capable in extracting valuable information from 3D structural models, as demonstrated in Jmol. Capabilities in Jmol enabled by Jmol SMILES and Jmol SMARTS include efficient MMFF94 atom typing, conformational identification, SMILES comparisons without canonicalization, identification of stereochemical relationships, quantitative comparison of 3D structures from different sources (including differences in Kekulization), conformational flexible fitting, and atom mapping used to synchronize interactive displays of 2D structures, 3D structures, and spectral correlations, where data are being drawn from multiple sources.