$ gemmi ss -h
Usage:
 gemmi ss [options] INPUT_FILE OUTPUT_FILE

Determines secondary structure of proteins using DSSP method.
Uses CCP4 monomer library to determine peptide bonds.


Options:
  -h, --help           Print usage and exit.
  -V, --version        Print version and exit.
  -v, --verbose        Verbose output.
  --monomers=DIR       Monomer library directory (default: $CLIBD_MON).
  -L CIF, --lib=CIF    User's restraint file(s). See more info below.
  --format=FORMAT      Input format (default: from the file extension).
  --calculate-h        Calculate hydrogen positions (original DSSP method).
                       Default: use existing H atoms.
  --hbond=TYPE         Hydrogen bond definition: energy (DSSP) or geometry
                       (distance+angle).
  --cutoff=DIST        Cutoff distance for neighbor search (default: 0.9 nm).
  --pihelix            Prefer pi-helices over alpha-helices.
  --polypro            Search for polyproline helices.
  --energy-cutoff=VAL  Hydrogen bond energy cutoff (default: -0.5 kcal/mol).
  --min-ca-dist=DIST   Minimum CA distance for hydrogen bonding (default: 9.0
                       A).
  --bend-angle=ANGLE   Minimum angle for bend assignment (default: 70.0
                       degrees).
  --hbonds=FILE        Output hydrogen bonds to a JSON file.
