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It depends on what you would want from the serialized objects. If you're not worried about human readability, pickle might be fine. Otherwise, something like JSON might be better. mBuild uses Google's protobuf but I don't exactly remember the motivations for doing so.
What is the use case? I'm not trying to shoot down my own idea I'm just trying to think it through. Create a system once and then reuse it for several different simulations? We don't need the system or moveset for mc.restart() anymore. The read frame analysis feature in Add load_final_frame to analysis module to facilitate MC-MD workflows #97 might require the System, depending on how it is implemented. Any other features/use cases that would require it? Also, given how closely related the System and MoveSet are, it might be dangerous to serialize them separately.
I don't think I care about it being human readable.
Is your feature request related to a problem? Please describe.
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