44 lines
1.7 KiB
Plaintext
44 lines
1.7 KiB
Plaintext
###############################################################################
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RosettaTR.py: Relax on dualspace (2 rounds of relax w/ different set of
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restraints)
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###############################################################################
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usage: RosettaTR.py [-h] [-r NRESTARTS] [-pd PCUT] [-m {0,1,2}] [-bb BB]
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[-sg SG] [-n STEPS] [--save_chk] [--orient] [--no-orient]
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[--fastrelax] [--no-fastrelax] [--roll] [--no-roll]
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NPZ FASTA OUT
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positional arguments:
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NPZ input distograms and anglegrams (NN predictions)
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FASTA input sequence
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OUT output model (in PDB format)
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optional arguments:
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-h, --help show this help message and exit
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-r NRESTARTS number of noisy restrarts (default: 3)
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-pd PCUT min probability of distance restraints (default: 0.05)
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-m {0,1,2} 0: sh+m+l, 1: (sh+m)+l, 2: (sh+m+l) (default: 2)
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-bb BB predicted backbone torsions (default: )
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-sg SG window size and order for a Savitzky-Golay filter (comma-
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separated) (default: )
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-n STEPS number of minimization steps (default: 1000)
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--save_chk save checkpoint files to restart (default: False)
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--orient use orientations (default: True)
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--no-orient
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--fastrelax perform FastRelax (default: True)
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--no-fastrelax
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--roll circularly shift 6d coordinate arrays by 1 (default: False)
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--no-roll
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# USAGE
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conda activate folding
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# try: -m 0,1,2
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# -pd 0.05, 0.15, 0.25, 0.35, 0.45
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# repeat ~3-5 times for every combination of -m and -pd
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# !!! use '--roll' option if no-contact bin is the last one !!!
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python ./RosettaTR.py -m 0 -pd 0.15 fake.npz fake.fa model.pdb
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