scripting_documentation/RosettaScripts/xsd/loop_definer_LoopsDatabase

Autogenerated Tag Syntax Documentation:

Load the loop defintions from a table in a database; the table from which this LoopsDefiner reads may be specified, but if it is not then it will look for a table named 'loops'. Beause of the way the apply function is written, this class is specific for JD2, which is a shame; it will have to be updated for JD3.

<LoopsDatabase name="(&string;)" database_table="(loops &string;)"
        db_session_name="(&string;)"
        transaction_mode="(standard &database_transaction_mode_string;)"
        database_mode="(&database_mode_string;)" database_name="(&string;)"
        database_pq_schema="(&string;)"
        database_separate_db_per_mpi_process="(&bool;)"
        database_partition="(&integer;)" database_read_only="(&bool;)"
        database_host="(&string;)" database_user="(&string;)"
        database_password="(&string;)" database_port="(&non_negative_integer;)"
        batch_description="(&string;)" protocol_id="(&non_negative_integer;)"
        batch_id="(&non_negative_integer;)" use_transactions="(&bool;)"
        cache_size="(2000 &non_negative_integer;)"
        remove_xray_virt="(false &bool;)"
        relevant_residues_mode="(explicit &report_to_db_relevant_residues_mode;)" />

database_table: The name of the table in the database from which the loops are to be read
db_session_name: The name for the (previously declared) DatabaseSession object to retrieve from the DataMap; if this option is given, then it will take precedence over the other database-session-defining attributes that are also allowed for this element. DatabaseSession objects are declared in the DATABASE_SESSIONS top-level block in RosettaScripts.
transaction_mode: Transaction mode for database output
database_mode: Which type of output database to use?
database_name: Name of output database
database_pq_schema: Schema name within the database
database_separate_db_per_mpi_process: Use a separate database for each MPI process? (sqlite3 only.) Incompatible with database_partition.
database_partition: Database partition to use. (sqlite3 only.) Incompatible with database_separate_db_per_mpi_process.
database_read_only: Is the database read-only? (sqlite3 only)
database_host: URI to the database server (postgres and mysql only)
database_user: Username for database access( postgres and mysql only)
database_password: Password for database access (postgres and mysql only)
database_port: Port to use for access to database server (postgres only)
batch_description: Description of features database
protocol_id: Manually controls protocol_id associated with this ReportToDB tag. Autoincrements by default.
batch_id: Manually controls the batch_id associated with this ReportToDB tag. Autoincrements by default.
use_transactions: Use transactions to group database i/o to be more efficient. Turning them off can help debugging.
cache_size: Specify the maximum number 1k pages to keep in memory before writing to disk.
remove_xray_virt: Remove virtual residue attached during xray refine process
relevant_residues_mode: Determine what features are reported given the relevant residues

scripting_documentation/RosettaScripts/xsd/loop_definer_LoopsDatabase_type