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Pipe protpardelle options through to the model #258

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@marcuscollins

Currently we only pass the ensemble size through to the actual Protpardelle model in the _run_guidance method (guidance_script_utils.py). We need to pipe more of the options through to control protpardelle more fully. Alternatively, some options may need to be passed through to the model when it is initialized as well.

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engineeringTask that is best suited to software engineers, not research scientists

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