SYBYL line notation

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sybyl line notation
Filename extension .sln
Type of format chemical file format

The SYBYL line notation or SLN is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SLN differs from SMILES in several significant ways. SLN can specify molecules, molecular queries, and reactions in a single line notation whereas SMILES handles these through language extensions. SLN has support for relative stereochemistry, it can distinguish mixtures of enantiomers from pure molecules with pure but unresolved stereochemistry. In SMILES aromaticity is considered to be a property of both atoms and bonds whereas in SLN it is a property of bonds.

Examples[edit]

Elemental atoms are specified by the standard abbreviation of the chemical elements. Atom attributes follow the atom name in square brackets. C[I=14] indicates carbon-14 isotope. Hydrogens are normally explicitly specified as a shorthand, CH4 is the SLN for methane. In addition to elemental atoms SLN supports the specification of wild card atoms: Any (match any atom), and Hev (match any heavy atom). It also has an extensive Markush syntax for specifying combinatorial libraries and RGROUP queries. SLN has several query atom types for matching groups of atoms. Each type has the group name, followed by an optional positive integer.

Group Description
R Used to match a side chain. Matched atoms must not have any connection to the core
X Used to match side chains and rings. Atoms matching an X group can match side chains and rings
Rx Matches side chains and rings, a ring closure must match a second Rx group

See also[edit]

References[edit]

  • Sheila Ash, Malcolm A. Cline, R. Webster Homer, Tad Hurst, and Gregory B. Smith, SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation, J. Chem. Inf. Comput. Sci., 1997, 37, 71–79. doi:10.1021/ci960109j
  • R. Webster Homer, Jon Swanson, Robert J. Jilek, Tad Hurst, and Robert D. Clark, SYBYL Line Notation (SLN): A Single Notation To Represent Chemical Structures, Queries, Reactions, and Virtual Libraries, J. Chem. Inf. Comput. Sci., 2008, 48, 2294–2307. doi:10.1021/ci7004687