Meta Features

A meta features reporter reports information about the batch of structures and the protocol that was used to generate it.

ProtocolFeatures

A protocol is represented as all the information necessary to reproduce the results of the Rosetta application execution. The features associated of each application execution are ultimately linked with a single row in the protocols table through the BatchFeatures reporter.

protocols :
- command_line : The complete command line used to execute Rosetta
- specified_options : The non-default options specified in the option system.
- svn_url : The url for the SVN repository used for the Rosetta source code.
- svn_version : The SVN revision number of the svn repository.
- script : The contents of the rosetta_scripts XML script if run via the rosetta_scripts system.

    CREATE TABLE IF NOT EXISTS protocols (
        protocol_id INTEGER PRIMARY KEY AUTOINCREMENT,
        command_line TEXT,
        specified_options TEXT,
        svn_url TEXT,
        svn_version TEXT,
        script TEXT);

BatchFeatures

    CREATE TABLE IF NOT EXISTS batches (
        batch_id INTEGER PRIMARY KEY AUTOINCREMENT,
        protocol_id INTEGER,
        name TEXT,
        description TEXT,
        FOREIGN KEY (protocol_id) REFERENCES protocols(protocol_id) DEFERRABLE INITIALLY DEFERRED));

JobDataFeatures

Store string , string - string , and string - real data associated with a job. As an example, the ligand docking code this way when it uses the DatabaseJobOutputter.

job_string_data
- data_key : Associate labeled keys with a structure

    CREATE TABLE IF NOT EXISTS string_data (
         struct_id INTEGER,
         data_key TEXT,
         FOREIGN KEY (struct_id) REFERENCES structures(struct_id) DEFERRABLE INITIALLY DEFERRED,
         PRIMARY KEY (struct_id, data_key));

job_string_string_data :
- data_key , data_value : Associate labeled text strings with a structure

    CREATE TABLE IF NOT EXISTS string_string_data (
         struct_id INTEGER,
         data_key TEXT,
         data_value TEXT,
         FOREIGN KEY (struct_id) REFERENCES structures(struct_id) DEFERRABLE INITIALLY DEFERRED,
         PRIMARY KEY (struct_id, data_key));

job_string_real_data :
- data_key , data_value : Associate labeled, real numbers with a structure

    CREATE TABLE IF NOT EXISTS string_real_data (
         struct_id INTEGER,
         data_key TEXT,
         data_value REAL,
         FOREIGN KEY (struct_id) REFERENCES structures(struct_id) DEFERRABLE INITIALLY DEFERRED,
         PRIMARY KEY (struct_id, data_key));

PoseCommentsFeatures

Arbitrary textual information may be associated with a pose in the form of (key, val) comments. The PoseCommentsFeatures reporter stores this information as a feature.

pose_comments : All pose comments are extracted using.

    CREATE TABLE IF NOT EXISTS pose_comments (
        struct_id INTEGER,
        key TEXT,
        value TEXT,
        FOREIGN KEY (struct_id) REFERENCES structures (struct_id) DEFERRABLE INITIALLY DEFERRED,
        PRIMARY KEY(struct_id, key));

RuntimeFeatures

Report how much time it took for each structure to be processed. The database is populated with two fields: a string 'timestamp' telling the date & time when the protocol started and an integer 'elapsed_time' telling the number of seconds that elapsed while the protocol was running.

Example:

<RuntimeFeatures/>

Options: None

Schema:

CREATE TABLE `runtimes` (
  `struct_id` bigint(20) NOT NULL DEFAULT '0',
  `timestamp` varchar(20) DEFAULT NULL,
  `elapsed_time` int(11) DEFAULT NULL,
  PRIMARY KEY (`struct_id`),
  FOREIGN KEY (`struct_id`) REFERENCES `structures` (`struct_id`)
)