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

Add hydrogens in positions specified by the monomer library.
By default, it removes and re-adds all hydrogens.
By default, hydrogens are not added to water.

Options:
  -h, --help       Print usage and exit.
  -V, --version    Print version and exit.
  -v, --verbose    Verbose output.
  --monomers=DIR   Monomer library dir (default: $CLIBD_MON).
  --format=FORMAT  Input format (default: from the file extension).
  --remove         Only remove hydrogens.
  --keep           Do not add/remove hydrogens, only change positions.
  --water          Add hydrogens also to waters.
  --sort           Order atoms in residues according to _chem_comp_atom.
