A Three-Pass Algorithm for Generation of BE-Matrices from IUPAC Names

A Three-Pass Algorithm for Generation of BE-Matrices from IUPAC Names

Sourav Mandal (Department of Computer Science and Technology, Bengal Engineering and Science University West Bengal, India) and Somnath Pal (Department of Computer Science and Technology, Bengal Engineering and Science University, Howrah, West Bengal, India)
DOI: 10.4018/ijcce.2013070103
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Abstract

One of the basic needs of chemoinformatics is to represents chemical compounds graphically in computer. Among several matrix representations of chemical graphs, BE-Matrix is one of the popular choices to represent molecules. There are several line notations available to input a chemical graph. Although several algorithms exist to convert from different line notations to suitable computer representations but using IUPAC Name, a line notation, to give input to the computer is not a popular method, because of the lack of suitable algorithm from IUPAC names to BE-Matrix or its variants. However, each and every chemist is familiar with IUPAC names, and therefore it calls for development of a suitable algorithm for such purpose. In this paper a three-pass algorithm for generating BE-Matrix from IUPAC name have been proposed and illustrated with suitable examples. The third pass of the algorithm can independently be used to convert from symbolic chemical names of any compound to BE-Matrix, thus making task of a chemist much simpler.
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Background

Graphical Representation

Chemical structure can be described using molecular graph, where the nodes are the atoms and the edges are the bonds between the two atoms and the number of the parallel edges denotes the bond order (Balaban, 1995; Schultz, 1989; Ivanciuc, 2003). Sometime in the molecular graph the hydrogen atom can be omitted. We can describe some properties of the atom in the nodes of the molecular graph (Ivanciuc, 2010). For example atom number or atom type can be added with the nodes and bond order with the edge of the molecular graph. These properties are very important when performing any kind of operation with or upon molecular graph. The graphical representation mainly describes the ways the nodes are connected that is the topology of the molecule. A graphical representation of di-methyl kitone or propanone is shown in Figure 1.

Figure 1.

Representation of di-methyl kitone or propanone as a labeled graph

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