alphafill-rebuild-db [options]


alphafill-rebuild-db is the program that creates a PostgreSQL database for the files processed by alphafill-process. This database is required for the web application.

This program will drop an already existing database and will recreate a new one and fill it with the information found. The db-* options are not required, the default user credentials are used if they are not specified.


Display the options allowed for this program.


Display the version of this program.


Use a more verbose output, printing status and progress information.


Do not print any status or progress information.


Use the file configfile to collection options. The default is to look for a file called alphafill.conf in the current directory and then in the directory /etc. Use this option to override this and specify your own configuration file.


Directory containing the alphafilled data


Directory containing the mmCIF files for the PDB


Pattern for locating structure files.

Default is ${db-dir}/${id:0:2}/AF-${id}-F${chunk}-filled_v${version}.cif.gz


Pattern for locating metadata files.

Default is ${db-dir}/${id:0:2}/AF-${id}-F${chunk}-filled_v${version}.cif.json


Pattern for locating PDB files.

Default is ${pdb-dir}/${id:1:2}/${id}/${id}_final.cif


AlphaFill database name


AlphaFill database owner


AlphaFill database password


AlphaFill database host


AlphaFill database port

See also

alphafill-create-index, alphafill-process, alphafill-server, alphafill.conf