Structural descriptors notations

Linear Notation is a type of structure descriptors strings that represent the 2D structure of a molecule as a set of characters, which represent the atoms in a linear manner, and symbols that are used to describe connectivity. 

Stereochemistry can be represented graphically in 2D structures, but also by (permutations) descriptors. It is included in all line notations and exchange formats. 

The assignment of descriptors and configuration is sometimes arbitrary, at best, when based on model structures and pseudo-atom coordination numbers. A more explicit stereochemical notation is achieved by using this notation, which states within the stereodescriptor the model structure on which the notation is based. In this notation the pseudo-square pyramidal structure is [5PF-5-14-C(i )]. This structure can be expected to result in geometric isomers when one of the... 

In order to calculate a physicochemical property, the structure of a molecule must be entered in some manner into an algorithm. Chemical structure notations for input of molecules into calculation software are described in Chapter 2, Section VII and may be considered as either being a 2D string, a 2D representation of the structure, or (very occasionally) a 3D representation of the structure. Of this variety of methods, the simplicity and elegance of the 2D linear molecular representation known as the Simplified Molecular Line Entry System (SMILES) stands out. Many of the packages that calculate physicochemical descriptors use the SMILES chemical notation system, or some variant of it, as the means of structure input. The use of SMILES is well described in Chapter 2, Section VII.B, and by Weininger (1988). There is also an excellent tutorial on the use of SMILES at www.daylight.com/dayhtml/smiles/smiles-intro.html. 

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 ... 

The SMILES descriptor is a simple way of encoding the molecular structure of a molecule, including any chiral centers. The method uses a line notation, with the ordinary alphabetic character set that is commonly found on every computer keyboard and results in a simple string commonly less than 15 characters. 

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