Options for using relational databases within Rosetta.
NOTE: Not to be confused with the option to specify the Rosetta database, which is found in the input options.
Currently supported backends include: sqlite3, mysql, and postgres
-inout:dbms:mode Specify database backend. default: 'sqlite3'
legal=["sqlite3", "mysql", "postgres"],
-inout:dbms:database_name If sqlite3, the filename for the database
-inout:dbms:pq_schema For PostgreSQL, the schema namespace in the database to use
-inout:dbms:host NOTE to use mysql or postgres as a backend:
-inout:dbms:user compile with 'extras=mysql' or 'extras=postgres' and use
-inout:dbms:password the '-inout:dbms:mode mysql' or
-inout:dbms:port the '-inout:dbms:mode postgres' flag
Consider using ~/.pgpass or ~/.my.cnf to store connection info-in:use_database Indicate that structures should be read from the given database
-in:select_structures_from_database An sql query to select which structures should be extracted.
ex: "SELECT tag FROM structures WHERE tag = '7rsa';"-out:use_database Write out structures to database.
Specify database via -inout:dbms:database_name and wanted structures with
-in:file:tags [Boolean]
-out:database_filter Filter to use with database output. Arguments for filter follow filter name [StringVector]
-out:resume_batch Specify 1 or more batch ids to finish an incomplete protocol.
Only works with the DatabaseJobOutputter.
The new jobs will be generated under a new protocol and batch ID