$ 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).
  --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.