OpenBabel contains function

Finally, any properties contained in the molfile will be stored in a separate table containing the text value copied from the file as well as a numeric value for the property, if that is appropriate for the property. There will be a one-to-many relationship between the structure and property table, allowing any number of properties to be stored for each structure. The function openbabel.molfile properties is shown in the Appendix. It expects a molfile and returns a composite data type, defined as follows. 

Create or Replace FUNCTION openbabel.contains(Bit, Bit) Returns Boolean As EOSQL ... 

The column structure.id is a unique integer relating the structure, sdf and property tables. The sdf.molfile column contains the molfile for each structure as defined by the vendor. The structure.name and structure.cansmiles columns contain the name and canonical smiles parsed and computed from the molfile. The structure.coord column will contain an array of atomic coordinates. The structure, atom column will contain an array of atom numbers from the file in canonical order to correspond to the atom order in the canonical SMILES. The OpenBabel/plpythonu extension functions molfile mol and molfile properties will be used to parse the vendor SDF molfiles and populate these tables. The molfile column of the sdf table is first populated from the SDF file, using the following perl script. 

This composite type is created when the openbabel schema and its associated functions are created using the code contained in the Appendix. It is not necessary to issue this SQL command again during the processing of the data from the vla-4.sdf file. 

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. 

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