alphafill-rebuild-db

Synopsis

alphafill-rebuild-db [options]

Description

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.

--help

Display the options allowed for this program.

--version

Display the version of this program.

--verbose

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

--quiet

Do not print any status or progress information.

--config=configfile

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.

--db-dir=dirname

Directory containing the alphafilled data

--pdb-dir=dirname

Directory containing the mmCIF files for the PDB

--structure-name-pattern=value

Pattern for locating structure files.

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

--metadata-name-pattern=value

Pattern for locating metadata files.

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

--pdb-name-pattern=value

Pattern for locating PDB files.

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

--db-dbname=name

AlphaFill database name

--db-user=name

AlphaFill database owner

--db-password=value

AlphaFill database password

--db-host=value

AlphaFill database host

--db-port=value

AlphaFill database port

See also

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