add _Base.additional_properties

[dsehnal]

@JonStargaryen I've added an easier way to set additional properties which doesn't require supporting it in every single builder function, where you can do something like:

builder.download(url=_url_for_mmcif(id))
        .parse(format="mmcif")
        .model_structure()
        .additional_properties(prop="test")  # sets prop of the parent model to "test"
        .component()
        .additional_properties(prop2="test2")  # sets prop2 of the parent component to "test2"
        .representation()

I wonder if we should make this the default method and remove the additional_properties: AdditionalProperties = None, from the constructor methods?