Chapter 11

3-Dimensional Molecular Structure Tables

In this chapter, various ways are discussed in which tables might be used to store 3-dimensional molecular structures. In these tables, each row represents a structure. The columns contain molecular properties, which may consist of arrays of atom properties. In previous chapters, the use of new data types was introduced to improve the way some data are stored and searched. Array data types were suggested as a way of storing atomic coordinates for a molecule. In this chapter, other ways will be shown in which molecular structures can be stored and searched in a RDBMS. These include the use of SMILES and entire files from external sources, such as molfiles or SDF files. Methods are shown to input, output, convert and search molecular structures from within the database. The SQL statements shown are valid in PostgreSQL, but may not be valid using other RDBMS. For example, the array data type is implemented differently in Oracle compared to PostgreSQL.Â