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class
jade.rosetta_jade.SetupRosettaOptionsBenchmark.SetupRosettaOptionsBenchmark(json_file)[source]¶ Bases:
jade.rosetta_jade.SetupRosettaOptionsGeneral.SetupRosettaOptionsGeneralClass for setting up Rosetta Benchmarks. See database/rosetta/benchmark_jsons_rabd/nstruct_test.json for an example.
Basically, a set of benchmarks and rosetta options are given in the JSON. Other keys can be specified for specific benchmarks (like the instructions file stuff in the above file.)
This can be used to use a single JSON file and run RosettaMPI on ALL combinations of benchmarks given.
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get_benchmark_names(only_rosetta=False)[source]¶ Get the names of all the benchmarks we will run.
Each benchmark must have a dictionary that defines ‘benchmarks’ as a list. You may optionally give the rosetta_option. Currently, your subclass of RunRosetta will need to code how all this is run. Hopefully, that will change.
If only_rosetta is true, will only give the benchmark names that are based on rosetta options.
For example:
- “outer_cycle_rounds”:{
- “rosetta_option”:”-outer_cycle_rounds”, “benchmarks”:[ 25, 50, 75, 100]
},
Return type: list
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get_benchmarks_of_key(benchmark_name)[source]¶ Get the list of benchmarks for a particular benchmark key. :param benchmark_name: str :rtype: list
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get_non_rosetta_option_benchmark_names()[source]¶ Similar to get_benchmark_names, but only for options which do not have the tag rosetta_option
Return type: list
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get_rosetta_option_of_key(benchmark_name)[source]¶ Get the Rosetta option :param benchmark_name: :rtype: str
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