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2016 ; 8
(ä): 50
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Jmol SMILES and Jmol SMARTS: specifications and applications
#MMPMID28316648
Hanson RM
J Cheminform
2016[]; 8
(ä): 50
PMID28316648
show ga
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.
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