Core function OpenBabel

There is an open-source extension of PostgreSQL called pgchem.7 It uses C functions and OpenBabel. It implements some of the core functions described in Chapter 7. The names of the functions are not the same as the names used here. Using pgchem, it should be possible to perform most of the operations represented by the core functions described in this book. 

Every one of these utilities will first require that a file of structures be loaded into a table in the database. Two methods are shown here importing a SMILES file and a mol file. Other file types could be added as needed, extending the core functions described earlier using mol file mol or molf ile to smiles as a model. OpenBabel is a good choice because of its support of many file formats. 

This Appendix contains structured query language (SQL) functions and tables too large or complex for the explanatory nature of the earlier chapters. 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 book, 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. 

Assume that the code above is stored in a file named openbabel-core.sql. In order to install these functions into a database named mydb, the following linux command would be used. 

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