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This looks promising - https://github.com/polysimtools/pysimm
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There are also more Chemistry-related libraries, like https://github.com/harirakul/chemlib, but that's more like modeling atoms/compounds, which seems different than what you're looking for.
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By what you described, the closest existing library according to what you need is Blockly (by Google), where you can create custom blocks, structure the "flow" of your script visually with the building blocks you pre-configured and then have the output in any supported language (JavaScript, Python...)
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Hence, a higher number means a more popular project.