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To implement v2.1, we need to do the following:
- Charged formulas
- Adduct and charge disambiguation
- Implement modification localization rules
- Better handling of unlocalized modifications
- Named layers
- Ambiguous colocalization control
We also should probably add a format version field to the ProForma object so we can keep track of which version(s) this is compatible with. Whether we try to robustly update to the latest format version is probably something we should control at the to_proforma function unless otherwise noted.
I think some of these can be handled incrementally, with adducts being the only major point of ambiguity, as everything else is either wholly backwards compatible or never occurs in earlier versions so we can't output something new from an existing input.
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