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