Most commands in MODELLER take one or more arguments, usually as Python keywords. For convenience, many of these arguments take a default value if you do not specify them.
Each argument must be of a specific type, either a MODELLER class object (e.g., a Model or Alignment) or one of the standard Python types (integers, strings, floating point numbers, or lists of these types).
Many commands take optional io and/or edat arguments. io should always be an IOData() object, and is used by commands that need to read coordinate files, while edat should be an EnergyData object, and is used by commands that need to use the energy function. For convenience, if these arguments are not specified, default values are taken from the MODELLER environment (Environ.io and Environ.edat respectively).