Creating a cavity database

The script, utilities/create_cavity_database/ may be used to build a cavity database from either PDB format files or from cavity XML files.

Optionally, a file containing PDB identifiers for processing a subset of the input files, or a maximum resolution limit may be supplied. Invoking the script with the option ‘-h’ shows the arguments required for usage.

The resulting database will be in SQLite format. It should be considered highly experimental; we do not guarantee that the schema or database format will remain the same in future releases.