$ gemmi contact -h
Usage:
 gemmi contact [options] INPUT[...]
Searches for contacts in a model (PDB or mmCIF).
  -h, --help     Print usage and exit.
  -V, --version  Print version and exit.
  -v, --verbose  Verbose output.
  -d, --maxdist=D  Maximal distance in A (default 3.0)
  --cov=TOL      Use max distance = covalent radii sum + TOL [A].
  --covmult=M    Use max distance = M * covalent radii sum + TOL [A].
  --minocc=MIN   Ignore atoms with occupancy < MIN.
  --ignore=N     Ignores atom pairs from the same: 0=none, 1=residue, 2=same or
                 adjacent residue, 3=chain, 4=asu.
  --nosym        Ignore contacts between symmetry mates.
  --assembly=ID  Output bioassembly with given ID (1, 2, ...).
  --noh          Ignore hydrogen (and deuterium) atoms.
  --nowater      Ignore water.
  --noligand     Ignore ligands and water.
  --count        Print only a count of atom pairs.
  --twice        Print each atom pair A-B twice (A-B and B-A).