###############################################################################
RosettaTR.py: Relax on dualspace (2 rounds of relax w/ different set of
        restraints)
###############################################################################


usage: RosettaTR.py [-h] [-r NRESTARTS] [-pd PCUT] [-m {0,1,2}] [-bb BB]
                    [-sg SG] [-n STEPS] [--save_chk] [--orient] [--no-orient]
                    [--fastrelax] [--no-fastrelax] [--roll] [--no-roll]
                    NPZ FASTA OUT

positional arguments:
  NPZ             input distograms and anglegrams (NN predictions)
  FASTA           input sequence
  OUT             output model (in PDB format)

optional arguments:
  -h, --help      show this help message and exit
  -r NRESTARTS    number of noisy restrarts (default: 3)
  -pd PCUT        min probability of distance restraints (default: 0.05)
  -m {0,1,2}      0: sh+m+l, 1: (sh+m)+l, 2: (sh+m+l) (default: 2)
  -bb BB          predicted backbone torsions (default: )
  -sg SG          window size and order for a Savitzky-Golay filter (comma-
                  separated) (default: )
  -n STEPS        number of minimization steps (default: 1000)
  --save_chk      save checkpoint files to restart (default: False)
  --orient        use orientations (default: True)
  --no-orient
  --fastrelax     perform FastRelax (default: True)
  --no-fastrelax
  --roll          circularly shift 6d coordinate arrays by 1 (default: False)
  --no-roll


# USAGE 
conda activate folding 

# try: -m 0,1,2
#      -pd 0.05, 0.15, 0.25, 0.35, 0.45
# repeat ~3-5 times for every combination of -m and -pd
# !!! use '--roll' option if no-contact bin is the last one !!!
python ./RosettaTR.py -m 0 -pd 0.15 fake.npz fake.fa model.pdb

