ReportToDB

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ReportToDB

Report structural data to a relational database using a modular schema. Each FeaturesReporter is responsible for a set of tables that conceptually represents a type of geometric, chemical, or meta property of a structure. All features reportered though a single instance of the ReportToDB Mover will be grouped into a batch of structures.

<ReportToDB name="&string" {database_connection_options}  cache_size="(&integer)" batch_description="&string" protocol_id="(&integer)" task_operations="(&task_operations)" relevant_residues_mode="[explicit,implicit]">
   <&string {feature_specific_options}/>
   <&string {feature_specific_options}/>
   .
   .
   .
</ReportToDB>

ReportToDB Tag :

name (&string) : The name assigned to this mover to be referenced in the MOVERS section of the RosettaScript.
database_connection_options : Options to connect to the relational database
sample_source (&string) : A description for the batch of structures. This ends up in the description column of the batches table.
task_operations : Restrict extraction of features to a subset of residues in a structure. A residue is relevant if it is packable . For multi-residue features, all residues must be packable for it to be reported.
relevant_residues_mode [ explicit default , implicit ]: Determines which features should be reported given the set of relevant residues. With explicit all residues in a feature must be relevant to be reported. With implicit at least one residues in a feature must be relevant to be reported.

Feature Subtags : Each features subtag applies a features reporter to the structure.

name (&string) : This is the name of the feature, e.g. RotamerRecoveryFeatures .
feature_specific_options : See individual FeaturesReporters to for details.
The following FeaturesReporters are included automatically:
- ProtocolFeatures : About the Rosetta application execution.
- BatchFeatures : About the set of features extracted by this ReportToDB instance.
- StructureFeatures : About each structure reportered by this ReportToDB instance. Note, currently each structure has a universally unique id, struct_id that is used as a composite primary key in almost all feature tables.
The following tables are created to help organize the features database:
- features_reporters : The FeaturesReporters used in any batch in the database

    CREATE TABLE IF NOT EXISTS features_reporters (
        report_name TEXT,
        PRIMARY KEY (reporter_name));

batch_reports : The features reporters used by this ReportToDB instance.

    CREATE TABLE IF NOT EXISTS batch_reports (
        report_name TEXT,
        batch_id INTEGER,
        FOREIGN KEY (report_name) REFERENCES features_reporters (report_name) DEFERRABLE INITIALLY DEFERRED,
        PRIMARY KEY (report_name, batch_id));

Additional Information:

General information using the a features database to do features analysis .
How to create a new FeaturesReporter.
Usage of features analysis for doing scientific benchmarking of the Rosetta ScoreFunction.

ReportToDB

ReportToDB

See Also