gc3libs.application.rosetta¶
Specialized support for computational jobs running programs in the Rosetta suite.
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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.
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terminated
()¶ Extract output files from the tar archive created by the ‘rosetta.sh’ script.
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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.