39 lines
2.1 KiB
Python
39 lines
2.1 KiB
Python
import argparse
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def get_args(params):
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parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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parser.add_argument("NPZ", type=str, help="input distograms and anglegrams (NN predictions)")
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parser.add_argument("FASTA", type=str, help="input sequence")
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parser.add_argument("OUT", type=str, help="output model (in PDB format)")
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parser.add_argument('-r', type=int, dest='nrestarts', default=params['NRUNS'], help='number of noisy restrarts')
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parser.add_argument('-pd', type=float, dest='pcut', default=params['PCUT'], help='min probability of distance restraints')
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parser.add_argument('-m', type=int, dest='mode', default=2, choices=[0,1,2], help='0: sh+m+l, 1: (sh+m)+l, 2: (sh+m+l)')
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parser.add_argument('-bb', type=str, dest='bb', default='', help='predicted backbone torsions')
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parser.add_argument('-sg', type=str, dest='sg', default='', help='window size and order for a Savitzky-Golay filter (comma-separated)')
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parser.add_argument('-n', type=int, dest='steps', default=1000, help='number of minimization steps')
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parser.add_argument('--save_chk', dest='save_chk', default=False, action='store_true', help='save checkpoint files to restart')
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parser.add_argument('--orient', dest='use_orient', action='store_true', help='use orientations')
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parser.add_argument('--no-orient', dest='use_orient', action='store_false')
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parser.add_argument('--fastrelax', dest='fastrelax', action='store_true', help='perform FastRelax')
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parser.add_argument('--no-fastrelax', dest='fastrelax', action='store_false')
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parser.add_argument('--roll', dest='roll', action='store_true', help='circularly shift 6d coordinate arrays by 1')
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parser.add_argument('--no-roll', dest='roll', action='store_false')
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parser.set_defaults(use_orient=True)
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parser.set_defaults(fastrelax=True)
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parser.set_defaults(roll=False)
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args = parser.parse_args()
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params['PCUT'] = args.pcut
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params['USE_ORIENT'] = args.use_orient
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params['NRUNS'] = args.nrestarts
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params['ROLL'] = args.roll
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params['NPZ'] = args.NPZ
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params['BB'] = args.bb
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params['SG'] = args.sg
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return args
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