Linear line notations

Topological indices are used to describe some components of connectivity. A more complete description is afforded by unidimensional codes (linear line notations) such as SMILES. Connectivity plus explicit attention to valence electrons is afforded by the electrotopological indices... 

Wiswesser line notation The Wiswesser line-formula notation (WLN) is a method for expressing the more usual graphical structure of a chemical compound as a linear string of symbols. The resulting alternative notation is unambiguous, short and particularly suitable for computer processing and retrieval but can also be understood easily by chemists after minimal training in its use. 

Line notations represent the structure of chemical compounds as a linear sequence of letters and numbers. The lUPAC nomenclature represents such a kind of line notation. However, the lUPAC nomenclature [6] makes it difficult to obtain additional information on the structure of a compound directly from its name (see Section 2.2). 

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. 

An alternative way to represent molecules is to use a linear notation. A linear notation uses alphanumeric characters to code the molecular structure. These have the advantage of being much more compact than the connection table and so can be particularly useful for transmif-ting information about large numbers of molecules. The most famous of the early line notations is the Wiswesser line notation [Wiswesser 1954] the-SMILES notation is a more recent example that is increasingly popular [Weininger 1988]. To construct the Wiswesser... 

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. 

Until the late 1970s, the Wiswesser Line Notation (WLN) was the only widely recognized format in which to code chemical structures in a computer-readable linear format. It was invented by William J. Wiswesser (1952), and his work was recognized and honored with the Skolnik Award for outstanding contributions to and achievements in the theory and practice of chemical information science by the American Chemical Society in 1980. The WLN was quickly adopted by major chemical companies to store and retrieve machine-readable, 3D-chemical structure information in a 2D, linear array, and is still in use today. 

There are several linear canonical notations for the input of chemical structures into the computer notable among these are the Wiswesser line notation [226] and the IUPAC notation [227], which are used in industrial information systems. In order to achieve a canonical notation, a large number of rules are necessary, more than three hundred in the Wiswesser line notation [226]. Furthermore, the resulting notation is quite arbitrary and very far from the usual practice of a chemist for example, acetone is 1V1 in the Wiswesser notation. In conclusion, both coding a formula and reading a coded formula in the Wiswesser notation require highly trained chemists. 

S YBYL Line Notation (Ash et al. 1997) is a linear format that to some extent resembles SMILES. The most important feature that these two formats have in common is human readability. However, the authors of SLN have made several design decisions that make it different from SMILES in several important points ... 

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. 

Access to all this information is provided by the Index Chemicus Registry System (ICRS), which contains records of new compounds and associated data on magnetic tape (6). Structures are described by the Wiswesser Line Notation (7), a system for describing chemical formulas in terms of a linear groups of symbols. A recent development is the ICRS Substructure Index (G5), which enables manual searches to be made for new chemical information, and is based on the occurrence of fragments of structures, the most common of which are illustrated as conventional structural diagrams. 

Two-dimensional representations alternative to the molecular graph are the linear notation systems, like, for example, Wiswesser Line Notation system (WLN) [Smith and Baker, 1975] and SMILES notation [Weininger, 1988 Weininger etal., 1989 Wei-ninger, 1990 Convard et al, 1994 Hinze and Welz, 1996]. 

Another approach for representing 2D chemical structures is the linear notation. Linear notations are strings that represent the 2D structure as a more or less complex set of characters and symbols. Characters represent the atoms in a linear manner, whereas symbols are nsed to describe information about the connectivity [3]. The most commonly nsed notations are the Wiswesser line notation (WLN) and the simpUfled molecnlar inpnt line entry specihcation (SMILES) [2]. The WLN, invented by William J. Wiswesser in the 1949, was the hrst line notation capable of precisely describing complex molecnles [4]. It consists of a series of uppercase characters (A-Z), numerals (0-9), the ampersand ( ), the hyphen (-), the oblique stroke (/), and a blank space. 

Two-dimensional representations alternative to the molecular graph are the linear notation systems, for example, Wiswesser Line Notation system (WLN) [Smith and Baker, 1975], SMILES [Weininger, 1988, 1990, 2003 Weininger, Weininger et al., 1989 Convard, Dubost et al., 1994 Hinze and Welz, 1996], and SMARTS (SMART - Daylight Chemical Information Systems, 2004). CAST (CAnonical representation of STereochemistry) is a method that gives a linear notation that canonically represents stereochemistry around a specific site in a molecule [Satoh, Koshino et al, 2000, 2001, 2002],... 

Line notations represent chemical structures as linear strings of alphanumeric symbols. Though the earliest ones were developed for use as manual ciphering... 

Briefly, notation systems attempt to record full, multidimensional structural descriptions in a linear form, by the use of more comprehensive symbols than atoms and bonds (e.g. symbols for particular chains, rings, functional groups). Thus, more information is recorded implicitly, in Uie rides of the notation, and less is recorded explicitly in the notations for individual compounds. The rules can therefore be quite complicated, in order to ensure the notations are unique and unambiguous. For the Wiswesser Line Notation, the rules are given in Smith, E. G. The Wis-wesser Line-Formula Chemical Notation. New York McGraw-Hill 1968. In this notation, for example, saturated carbon chains are simply indicated by an arable numeral equal to the number of carbons in the chain, branch-... 

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. 

Figure 3. Linear representations of graphical formula standardized chemical nomenclature and Wiswesser Line Notation ...

Draw the linear alkane with six carbons, using line notation. 

All molecules discussed in this chapter will contain only carbon and hydrogen. There are linear chains of carbon atoms, and carbons can branch from the linear chain. The carbon branches are known as alkyl groups. Line notation is used to draw linear alkanes as well as branched alkanes. For example, 4A is identical to 4, 5A is identical to 5, and 6A is identical to 6. Structure 4A is a three-carbon alkane, and 5A is a four-carbon alkane where the carbons are connected in a linear chain. For 6A, there is a five-carbon linear chain, with two one-carbon groups attached to that chain. 

SMILES - simplified molecular line entry specification. A very terse linear notation which is much easier to create and to decode than the notorious WLN (Wiswesser line notation). Variations of SMILES include SSMILES, USMILES, SMARTS, SMIRKS, STRAPS, GHUGKLES, GHORTLES, and GHARTS which add features such as substructure search operators, reactions, combinatorial chemistry, and unique naming. ... 

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