Molecular representations structures

The most well-known and at the same time the earliest computer model for a molecular structure representation is a wire frame model (Figure 2-123a). This model is also known under other names such as line model or Drciding model [199]. It shows the individual bonds and the angles formed between these bonds. The bonds of a molecule are represented by colored vector lines and the color is derived from the atom type definition. This simple method does not display atoms, but atom positions can be derived from the end and branching points of the wire frame model. In addition, the bond orders between two atoms can be expressed by the number of lines. 

Ferk, V., Blejec, A., Gril, A. (2003). Students understanding of molecular structure representations./ /ema/ro a/JoMr a/of 5cze ceii rferca//oM, 25(10), 1227-1245. 

This example demonstrates the possibility of hypergraph modeling for molecular structure representation with the different degrees of accuracy. 

Todeschini, R., Consonni, V., Galvagni, D. and Gramatica, P. (1999). A New Molecular Structure Representation Spectral Weighted Molecular (SWM) Signals for Studies of Molecular Similarity. Quimica Analitica, 18, 41-47. 

For those of you interested in Prolog, the book "Prolog Programming in Depth" (34), has a good discussion of program debugging and verification, as well as an example representation in Prolog of a connectivity table for molecular structure representation. 

I. Canonicalization of the Molecular Structure Representation Basically, canonicalization consists of numbering the... 

W.T. Wipke H) first achieved the canonicalization of a molecular structure representation in a computer program that includes all aspects of stereochemistry. In some other schemes, stereochemistry is not invoked to aid in the mambering of the atoms. Such schemes are incomplete. If we relegate stereochemistry to a footnote and the numbering of the atoms and the connection tables of two isomers can be the same, then we lose most of the above-stated advantages of canonicalizing. 

The reactant generation time for difficult problems, e.g. steroids, is 4-5 milliseconds, hence the programs spend as much as 40% of their time canonicalizing the molecular structure representation. Evidently, here is the most important place to think about efficiency. 

Of the chemical data categories in Figure 2 the molecular structure representation has received by far the greatest emphasis in current Information systems. The other data types (analytical, physicochemical, process development, synthesis/reactivlty) have been dealt with Individually, but are only beginning to be Incorporated with the structure files to form integrated systems. 

Based on group contributions. Relies on the idea that a molecule acts as a number of fragments (atoms, bonds, moieties,...) independently contributing to the investigated property, usually by an additive scheme. Yet, many of these methods are of questionable accuracy and have limited applicability due to the oversimplification of the molecular structure representation. [2]... 

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