application: hetparse [
  documentation: "Converts heterogen group dictionary to
                  EMBL-like format."
  groups: "Utils:Database creation"
  gui: "yes"
  batch: "yes"
  cpu: "low"
  embassy: "structure"
]

section: input [
  information: "Input section"
  type: "page"
]

  infile: infile [
    parameter: "Y"
    information: "Raw dictionary of heterogen groups file"
    help: "This option specifies the name of input file (raw
           dictionary of heterogen groups) to parse, which should be of the
           format specified at http://pdb.rutgers.edu/het_dictionary.txt"
    knowntype: "Raw dictionary of heterogen groups"
  ]

  toggle: dogrep [
    standard: "Y"
    information: "Search a directory of PDB files with
                  keywords?"
    help: "This option specifies whether to search a directory of
           files (typically PDB files) with keywords. If set, HETPARSE will
           search the directory and will count the number of files that each
           heterogen appears in."
    default: "N"
  ]

  dirlist: dirlistpath [
    standard: "$(dogrep)"
    information: "Pdb entry directories"
    help: "This option specifies the directory to search with
           keywords."
    default: "./"
    extension: "ent"
    knowntype: "pdb"
  ]

endsection: input

section: required [
  information: "Required section"
  type: "page"
]

endsection: required

section: output [
  information: "Output section"
  type: "page"
]

  outfile: outfile [
    parameter: "Y"
    default: "Ehet.dat"
    information: "Dictionary of heterogen groups output file"
    help: "This option specifies the name of EMBL-like format
           dictionary of heterogen groups."
    knowntype: "Dictionary of heterogen groups"
  ]

endsection: output
