Molalign command line help

usage: ./molalign -s SMARTS [-h] [-v] [-fs string] [-1 #] [-2 #] [-3 #] [-a sdf|rdf|x|y] [-o smi|sdf] [-p] [-v]
 Reads on stdin:
 (if -a rdf or -p or -s @rdf) an rdf file with product coords,
 (if -a rdf or -p or -s @rdf) cat'ed to a unique file separator string
  cat'ed to an sdf file with many product molecules.
 Writes on stdout a sdf file of many product molecules
  with coords rotated to conform to target (see -a).
  -s SMARTS: SMARTS defining alignment atoms
  -s "@sdf": SMARTS will be SMILES  of first sdf molecule
  -s "@rdf": SMARTS will be SMILES (or variants thereof) of first rdf product
  -h: this brief help
  -fs string: unique string marking end of rdf file (default END-OF-RDF-FILE)
  -1 #: 1st atom in smarts (or in rdf if -s @rdf) to align (default=1)
  -2 #: 2nd atom in smarts (or in rdf if -s @rdf) to align (default=2)
  -3 #: 3rd atom in smarts (or in rdf if -s @rdf) to align (default=3)
  -a: align to [rdf][sdf][x][y]
      sdf: align to sdf first molecule coordinates (default)
      rdf: align to rdf first product coordinates
      x: align to x axis
      y: align to y axis
  -o: [smi][sdf] output file format
      sdf : output sdf (default)
      smi: output smiles
  -p: include rdf product core in output sdf file (ignored unless -o sdf)
  -v: diagnostic verbosity on stderr