Appendix - Design and Use of Relational Databases in Chemistry - page 173

Appendix
A.1 Introduction
This Appendix contains structured query language (SQL) functions and
tables too large or complex for the explanatory nature of the earlier chap-
ters. These functions and tables are practical, rather than explanatory. They
all follow PostgreSQL syntax. Some of them require the core functions
described in Chapter 7 of this topic, for example, match , cansmiles , and
count _ matches . Those functions are available in the CHORD product
from gNova, Inc. This Appendix also contains a PerlMol implementation,
a FROWNS implementation, and an OpenBabel implementation of the
core functions for PostgreSQL.
A.2 Symbols and Bonds from
Simplified Molecular Input Line
Entry System (SMILES)
If SMILES is used to store molecular structures in a relational database
management system(RDBMS), it may be necessary to extract the symbol
and bond information for some client programs that expect a connection
table. The smiles _ to _ symbol and smiles _ to _ bonds function
shown in the next sections allow the symbol and bond information in
a SMILES to be extracted as an array. Some client programs may prefer
to process this information in rows, as if they were records in a file. The
following plpgsql functions can be used to present the array elements as
rows. Two functions are shown: ctable (connection table) and symbol_
coords. The symbol _ coords function requires an array of coordinates
in addition to the symbols.
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