$ 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 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).
  --sort             Order atoms in residues according to _chem_comp_atom.
  --update           If deprecated atom names (from _chem_comp_atom.alt_atom_id)
                     are used in the model, change them.
  --d-fract=FRACT    Add atoms as H/D mix, with the given deuterium fraction.
Hydrogen options, mutually exclusive. Default: add hydrogens, but not to water.
  --water            Add hydrogens also to water.
  --unique           Add only hydrogens with uniquely determined positions.
  --keep             Do not add/remove hydrogens, only change positions.
  --no-change        Do not change hydrogens, not even positions.
  --remove           Only remove hydrogens.

Option -L/--lib can be used multiple times, in order of priority.
Its argument is either a file path or one of the two special values:
    '+' = monomer blocks in mmCIF INPUT_FILE (ignored by default)
    '@' = the priority of the monomer library (ML, default: lowest)
Example 1:   -L file.cif -L+    order: file.cif, input file, ML
Example 2:   -L@ -L file.cif    order: ML, file.cif
