scripting_documentation/RosettaScripts/xsd/to_ReadResfileFromDB_type

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Autogenerated Tag Syntax Documentation:

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This task operation will query a database for a resfile string. The table in the database should have a column named 'resfile' and a (key) column named 'tag'. The 'selection_tag' attribute for this task operation should be used to say which row to query from the database.

<ReadResfileFromDB name="(&string;)" residue_selector="(&string;)"
        database_table="(&string;)" table="(&string;)"
        selection_tag="(&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;)" />

• residue_selector: If this is used, then the ResidueSelector is used as a mask, and the ReadResfile TaskOperation is applied only to those residues selected by the ResidueSelector, even if the resfile lists other residues as well. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
• database_table: The table in the database from which to read
• table: The table in the database from which to read (same as database_table)
• selection_tag: (REQUIRED) The tag to use to identify the row in the indicated table that will be read from for the indicated job. In JD3, this can/should be combined with the script_vars flag so that different jobs can read different resfiles. This is a marked departure from the JD2 functionality which relied on the global data representing the currently-running job. That functionality is now removed.
• 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

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