Structure representation line notations

The ROSDAL (Representation of Organic Structures Description Arranged Linearly) syntax was developed by S. Welford, J. Barnard, and M.F. Lynch in 1985 for the Beilstein Institute. This line notation was intended to transmit structural information between the user and the Beilstein DIALOG system (Beilstein-Ohlme) during database retrieval queries and structure displays. This exchange of structure information by the ROSDAL ASCII character string is very fast. 

Chemical structures can be transformed into a language for computer representation via line notations such as ROSDAL, SMILES, Sybyl. 

The problem of perception complete structures is related to the problem of their representation, for which the basic requirements are to represent as much as possible the functionality of the structure, to be unique, and to allow the restoration of the structure. Various approaches have been devised to this end. They comprise the use of molecular formulas, molecular weights, trade and/or trivial names, various line notations, registry numbers, constitutional diagrams 2D representations), atom coordinates (2D or 3D representations), topological indices, hash codes, and others (see Chapter 2). 

Figure 6-1. Different forms of representation of a chemical graph a) labeled (numbered) graph b) adjacency matrix c) connectivity table, type I d) connectivity table, type II f) line notations g) structural index.

Eakin [13] describes the chemical structure information system at Imperial Chemical Industries Ltd., where registration is based on Wiswesser Line Notation. For connection tables, the unique, unambiguous representation is derived automatically, i.e., a single, invariant numbering of the connection table is algorithmically derived. 

Programs now exist to convert Wiswesser Line Notation [29], Hayward [30], and IUPAC [18] linear notations to connection tables. Because fragment codes alone do not provide the complete description of all structural detail, conversion to other representations is typically not possible. 

Computer-Aided Property Estimation Computer-aided structure estimation requires the structure of the chemical compounds to be encoded in a computer-readable language. Computers most efficiently process linear strings of data, and hence linear notation systems were developed for chemical structure representation. Several such systems have been described in the literature. SMILES, the Simplified Molecular Input Line Entry System, by Weininger and collaborators [2-4], has found wide acceptance and is being used in the Toolkit. Here, only a brief summary of SMILES rules is given. A more detailed description, together with a tutorial and examples, is given in Appendix A. 

The last two lines are new, compared to the text output without the -p option and are a rough measure for the well-definedness of the MFE structure. The line before the last line shows a condensed representation of the pair probabilities, similar to the bracket notation, followed by the ensemble free energy in kcal mol-1. The structure string contains additional symbols coding for the pairing tendency of that position. 

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. 

These identifiers were developed as an lUPAC project in 2000-2004. They are the most recent technology aimed at an unambiguous text-string representation of chemical structures. (Earlier technologies included Wiswesser line notation, which is not described here, and SMILES, described below.)... 

A descriptor center finally consists of a structural part (e.g., atom, multiple similar atoms, pseudoatoms, fragments) and a property. To define this structural part efficiently, the line notation SLang is used, which is similar to simplified molecular input line enky specification (SMILES) and SMILES arbitrary target specification (SMARTS) [12]. Examples for structural parts and their representations in SLang are as follows ... 

Figure 6.1 A simple chemical structure and its representation in several different line notations.

The lUPAC International Chemical Identifier (InChl) is a relatively recent arrival on the chemical structure representation scene, and combines some of the characteristics of connection table, line notation and registry number identifier. A comprehensive technical description has yet to be published, though substantial details are given in the documentation which accompanies the open-source software provided by lUPAC, and a number of authors have provided good overviews. " ... 

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. 

Kekule structure Representation using a line notation for bonding electrons, with lone pairs shown by dots or omitted. 

The efforts in computer technology were based on non-graphic business applications, so it was most practical for the chemical information systems to be made to adapt to the standard business computer. Systems evolved that were based on linear representations of graphical formulas, such as Wiswesser Line Notation, WLN (see Figure 3), or standard chemical nomenclature. But the linear representations were one step further removed from the 2-D structure that the chemist so depended on, and involved learning what in essence was a foreign language. The chemists found themselves more and more alienated from their own literature, and information intermediaries found their place in the sun. 

We have defined above what we mean by structures, the ordinary line notation used by organic chemists wherein we rely on a string representation with branching indicated by parenthesization. The reader will recall that context free grammars allow more complicated nested productions, e.g. S aSb than are allowed for by regular productions. Consider grammar 3 below ... 

Draw the structure for each of the following using line notation (the extended or zigzag representation) ... 

Computer representations of chemical structures have been used since the 1950s. With the dramatic reduction in the cost of computer storage over the past two decades, storage forms such as line notations have given way to the less compact atom-bond connection table, in which the atoms and bonds contained in the structure are explicitly listed, often in tabular form. Line notations still retain some applications, mainly as rapid input formats. 

In Summary Determination of organic structures relies on the use of several experimental techniques, including elemental analysis and various forms of spectroscopy. Molecular models are useful aids for the visualization of the spatial arrangements of the atoms in structures. Condensed and bond-line notations are useful shorthand approaches to drawing two-dimensional representations of molecules, whereas hashed-wedged fine formulas provide a means of depicting the atoms and bonds in three dimensions. 

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