This creates a new io_data object, with default parameters. You can, however, specify any of these parameters when you create the object:
io = io_data(hetatm=True)
Alternatively, you can set parameters in an existing object:
io.hetatm = True
Many commands use io_data objects. However, for convenience, the environ class also contains an io_data object, as environ.io. This is used as the default if you do not give an io_data parameter, so you can set this to change the input configuration used by all functions:
env = environ()
env.io.hetatm = True
Please note that io_data.hetatm, io_data.hydrogen and io_data.water are ignored when reading UHBD files. When reading CHARMM files, io_data.hetatm is ignored.