gc3libs.application.rosetta

Specialized support for computational jobs running programs in the Rosetta suite.

class gc3libs.application.rosetta.RosettaApplication(application, application_release, inputs, outputs=[], flags_file=None, database=None, arguments=[], **extra_args)

Specialized Application object to submit one run of a single application in the Rosetta suite.

Required parameters for construction:

• application: name of the Rosetta application to call (e.g., “docking_protocol” or “relax”)
• inputs: a dict instance, keys are Rosetta -in:file:* options, values are the (local) path names of the corresponding files. (Example: inputs={"-in:file:s":"1brs.pdb"})
• outputs: list of output file names to fetch after Rosetta has finished running.

Optional parameters:

• flags_file: path to a local file containing additional flags for controlling Rosetta invocation; if None, a local configuration file will be used.
• database: (local) path to the Rosetta DB; if this is not specified, then it is assumed that the correct location will be available at the remote execution site as environment variable ROSETTA_DB_LOCATION
• arguments: If present, they will be appended to the Rosetta application command line.

terminated()

Extract output files from the tar archive created by the ‘rosetta.sh’ script.

class gc3libs.application.rosetta.RosettaDockingApplication(pdb_file_path, native_file_path=None, number_of_decoys_to_create=1, flags_file=None, application_release='3.1', **extra_args)

Specialized Application class for executing a single run of the Rosetta “docking_protocol” application.

Currently used in the gdocking app.