FiltRest3D command line interface

shell$ filtrest3d.py --help
usage: filtrest3d.py [] (-r|--restraints)  [*] [*]

options:
  -h, --help            show this help message and exit
  -r RESTRAINTS_FILE, --restraints=RESTRAINTS_FILE
                        File with restraints description
  --limit=N             process at most N structures
  -d DIRFILE, --dirfile=DIRFILE
                        Path to file with list of PDB files, one path per
                        line.
  --silent=SILENTFILE   Path to Rosetta silent file ('.out' or '.out.gz') with
                        structures (contains just C-alpha + SS assignment
  --traf=TRAFFILE       Path to CABS TRAjectory file ('.tra' or '.traf')
  --seq=SEQFILE         Path to CABS SEQuence file complementing TRAjectory
                        information
  --fasta=FASTAFILE     Path to FastA sequence file complementing TRAjectory
                        information
  -l, --linear          Use linear punishment function for distance
                        restraints.
  -s, --sqrt            Use square punishment function for distance
                        restraints.
  --knotted             Assume protein has a knot.
  -k, --not-knotted     Assume protein has no knots.
  --check-solvation-prediction
                        Assume protein has no knots.
  --verbose             Print debug information.
  --debug-memory-use    print number of live objects after processing each
                        file
  -p PYMOL_SCRIPT, --pymol-script=PYMOL_SCRIPT
                        Output PyMol script for restraints visualization
  -v VMD_SCRIPT, --vmd-script=VMD_SCRIPT
                        Output VMD script for restraints visualization
  -i, --incremental     Print results as they are generated
  --model-pickle=MODEL_PICKLE
                        filename to put the pickle of PDB
  -o OUTPUT, --output=OUTPUT
                        write CSV output to file
  --run-pymol           run PyMol on first model and generated PyMol script
  --progress-bar        print dot for each parsed model