!BRIEF [options] [-ref <mol file>] [-in <mol file>] [-out <mol file>]

!CATEGORY "input/output options"

  !PARAMETER -ref
    !TYPE string
    !REQUIRED true
    !BRIEF input reference mol file name
    !KEYLESS 1
  !END

  !PARAMETER -in
    !ALIAS -i
    !TYPE string
    !REQUIRED true
    !BRIEF input mol file name
    !KEYLESS 2
  !END

  !PARAMETER -out
    !ALIAS -o
    !TYPE string
    !REQUIRED false
    !BRIEF output file name, this implies that -overlay should be true
    !KEYLESS 3
  !END

!END

!CATEGORY "options"

  !PARAMETER -automorph
    !TYPE bool
    !DEFAULT true
    !BRIEF assign best atom association
    !DETAIL
        If false, atoms are associated by order.
        If true, graph isomorphism is determined with symmetry perception.
  !END

  !PARAMETER -overlay
    !TYPE bool
    !DEFAULT true
    !BRIEF Minimize to the smallest RMSD
  !END

  !PARAMETER -heavyonly
    !TYPE bool
    !DEFAULT true
    !BRIEF Ignore hydrogens for RMSD calculation
  !END

  !PARAMETER -verbose
    !ALIAS -v
    !TYPE bool
    !DEFAULT false
    !BRIEF verbose
  !END

!END
