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One case that we can't currently handle is that of a catalyst, i.e. a reaction A + B -> A + C, since the stoichiometry for such a reaction would be (0, -1, +1), making it seem as if A doesn't participate at all.
I don't think this is an urgent case to address, but I thought I'd record the concern. One solution is to store reactants and products separately, e.g. (1, 1, 0) and (1, 0, 1) or similar.
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