class jade.rosetta_jade.BenchmarkInfo.BenchmarkInfo(decoy_path, full_name, final_name, scorefunction='talaris2014')

Simple Class for holding info for a particular benchmark. Parses the Run_Settings.txt file in the decoy directory. This file is output by RunRosettaBenchmarks.

The settings dictionary then holds key/value pairs. Here is an example of this file for RAbD:

CDR = ALL DATASET = bm2_ten DOCK = False INNER_CYCLE_ROUNDS = 1 INPUT_PDB_TYPE = pareto L_CHAIN = kappa MINTYPE = relax OUTER_CYCLE_ROUNDS = 100 PAPER_AB_DB = True PROTOCOL = even_cluster_mc RANDOM_START = True REMOVE_ANTIGEN = True SEPARATE_CDRS = False

get_dataset()

Get the dataset used for benchmarking. :rtype: str

get_decoy_path()

Get the directory of all of the decoys for this benchmark. :rtype:

get_final_name()

Get the final name of the benchmark (used mainly for features dbs or comparisons between benchmarks.) :rtype: str

get_full_name()

Get the full name of the benchmark. :rtype: str

get_input_pdb_type()

Get the input pdb type used, ex: native vs pareto :rtype: str

get_scorefunction_name()

Get the scorefunction name set in this info instance. :rtype: str

has_log_path()

jade.rosetta_jade.BenchmarkInfo.get_run_settings(dir, fname='RUN_SETTINGS.txt')

Gets a dict of the settings used to run the benchmark in the directory.

The settings file looks like this, and is output by RunRosettaBenchmarks into the decoy directory:

CDR = ALL DATASET = bm2_ten DOCK = False INNER_CYCLE_ROUNDS = 1 INPUT_PDB_TYPE = pareto L_CHAIN = kappa MINTYPE = relax OUTER_CYCLE_ROUNDS = 100 PAPER_AB_DB = True PROTOCOL = even_cluster_mc RANDOM_START = True REMOVE_ANTIGEN = True SEPARATE_CDRS = False

Parameters:dir – str Return type:defaultdict