Sybyl line notations

Atoms Atoms a e represented by their atomic symbols. Ambiguous two-letter symbols (e.g., Nb is not NB) have to be written in square brackets. Otherwise, no further letters are used. Free valences are saturated with hydrogen atoms. 

Bonds Single, double, triple, and aromatic (or conjugated) bonds are indicated by the symbols and respectively single and aromatic bonds should be omitted. 

Disconnected structures in the molecule Individual parts of the compound are separated by a period. The period indicates that there is no connection between atoms or parts of a molecule. The arrangement of the parts is arbitrary. 

Cyclic structures Rings are described by breaking the ring between two atoms and then labeling the two atoms with the same number. 

Aromaticity Aromatic structures are indicated by writing all the atoms involved in lower-case letters. 

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Imports data in SD file format, MDL molfile format, SMILES text strings, Daylight Chemical Information Systems Inc. s Thor Data Tree (TDT) format, and Tripos Inc. s Sybyl Line Notation (SLN) format. 

Ash, S., M.A. Cline, R. Webster Homer, T. Hurst, and G.B. Smith. 1997. SYBYL Line Notation (SLN) a versatile language for chemical structure representation. J. Chem. Inf. Comput. Sci. 37 71-79. 

SLN—Sybyl Line Notation. Linear notation used in conjunction with Tripos SPL (Sybyl Programming Language) to manipulate chemical structures. It is similar in syntax to SMILES notation. 

Generic or Markush structures are a form of structural representation that can be used to encompass many individual molecules having common structural features. Figure 6.5 shows a simple example. They are particularly associated with chemical patents,but may also be used (often with a table of values for the R-groups) to represent sets of related molecules involved in structure - activity relationship studies, or large combinatorial libraries. The RGfile variant of the Molfile format can represent restricted forms of Markush structure, as can Sybyl line notation,and a variety of vendors have implemented ad hoc extensions (which have some Markush capabilities) to SMILES. 

The SPL-Script csln create.spl for generating the combinatorial sybyl line notation (CSLN) ... 

A notation similar to SMILES is Sybyl Line Notation. It provides atom and bond attributes for tetrahedral and cis/trans stereogenic units. Internally, the system uses parities but it can automatically convert CIP (or Fischer) labels to this representation. 

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