Molecular descriptor notations

FREL fragment reduced to an environment that is limited [3] 

FRELb atom-centered substructure used with the LOGIC method [5] 

I mean mean information content (information theoretical index) [8] 

L/B length to breath of rectangle enclosing planar molecule [8,9] 

M molar mass (formerly known as molecular weight) 

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Wiswesser Line Notation system molecular descriptors... 

The following concepts deal with graph and molecule substructures. These are necessary for introducing molecular descriptors, which are relevant for the applications described in later chapters. Our notation is adapted to the notation commonly used in chemistry, and is slightly different from that in graph theory. 

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. 

Assembly descriptor a formula-like notation that expresses the number of binding sites and the topicity of molecular building units... 

The most simple filters are calculated directly from the molecular formula, from the element composition, or from an extended description of the atom types of a molecule. Extended atom types are notations of atoms that include more information than just the element name (e.g., level of hybridization, membership in a certain functional group, etc.). Many molecular properties are usable as filter descriptors [24-27]. 

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 ... 

Clearly, these prochiral and prostereotopic descriptors for paired ligands in molecules i-xv constitute a duplex system and, in any case, do not indicate the stereotopic relationships of the ligands in question. We propose an alternate, unified notation that specifies the concise stereotopicity of paired ligands on the one hand, and paired faces, on the other. The notation is further extended to accommodate the chirality of the molecular field (chirotopicity). 

MCDL available at http //mcdl.sourceforge.net/ is another free open-source small Java molecular viewer/editor for chemical stmctures, stored in Modular Chemical Descriptor Language linear notation only [26]. 

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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