Computer Representations of Molecular Structures - Design and Use of Relational Databases in Chemistry - page 71

chapter 7
Computer Representations
of Molecular Structures
7.1 Introduction
There are many ways to represent molecular structures. A drawing is per-
haps the most common and useful. It is easy to store drawings of molecules
in a computer, but a stored drawing does not constitute a useful computer
representation. What is needed is a computer representation that allows
structures to be stored and searched in chemically useful and meaningful
ways. This is sometimes accomplished by storing a connection table con-
taining atom and bond information. Additionally, two- or three-dimen-
sional coordinates are often stored. These data can be stored in files or
data structures in some computer language. This chapter introduces ways
of representing molecular structures that take advantage of the relational
model of data in a relational database management system (RDBMS).
According to standard valence bond theory, 1 the essential components
of a molecular structure are the atoms and bonds composing the molecule.
Two atomic properties are required—the atomic symbol or atomic num-
ber and the formal charge on the atom. Other atomic properties might be
useful in many applications but are not considered as essential for the dis-
cussion in this chapter. The two atoms participating in a bond define the
bond. A bond type, namely single, double, or triple, completes the defini-
tion of a bond. It is frequently convenient to use the notion of aromaticity 2
to further classify bonds and even the atoms composing that bond. The
concept of a hydrogen bond is not considered here.
Files, such as SDF molfiles3 3 or PDB 4 files are commonly used to rep-
resent molecular structures. The data in these files contain information
about the atoms, atom charges and aromaticity, and bonds between the
atoms. It is possible to define a relational table where each of the data
fields in the file is stored in a separate column. One could write structured
query language (SQL) to store and search data in such tables, but there is
a more succinct way to represent the same information.
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