appl: pepnet [
  documentation: "Displays proteins as a helical net"
  groups: "Display, Protein:2D Structure"
]

section: input [ info: "input Section" type: page ]
sequence: sequence  [
  parameter: "Y"
  type: "Protein"
]

endsection: input

section: output [ info: "output Section" type: page ]
bool: amphipathic  [
  information: "Prompt for amphipathic residue marking"
  help: "If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked. This overrides any other markup that you may have specified using the qualifiers '-squares', '-diamonds' and '-octags'."
]

string: squares  [
  optional: "@(!$(amphipathic))"
  default: "ILVM"
  information: "Mark as squares"
  help: "By default the aliphatic residues ILVM are marked with squares."
]

string: diamonds  [
  optional: "@(!$(amphipathic))"
  default: "DENQST"
  information: "Mark as diamonds"
  help: "By default the residues DENQST are marked with diamonds."
]

string: octags  [
  optional: "@(!$(amphipathic))"
  default: "HKR"
  information: "Mark as octagons"
  help: "By default the positively charged residues HKR are marked with octagons."
]

bool: data  [
  required: "N"
  default: "N"
  information: "Display as data"
  help: "Output the data to a file instead of plotting it"
]

graph: graph  [
  required: "@(!$(data))"
]

endsection: output

