Specialized support for computational jobs running programs in the Rosetta suite.
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:
- outputs: list of output file names to fetch after Rosetta has finished running.
- 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
- arguments: If present, they will be appended to the Rosetta application command line.
Extract output files from the tar archive created by the ‘rosetta.sh’ script.
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.