Data: annotate post-2020 reactions with pathways; port the step that was lost in 2020 - #300

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freiburgermsu:nar2026-annotate-post2020-reactions

Commits on Sep 24, 2026

Derive an InChI's formula and charge from its own layers, not from a parser

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f7d6d79
Validate protonation rows against what a protonation can do; repair the ones that fail

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6e51b7d
Marvin 26.1 bundle: replace the 130 rows that are not protonations

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Marvin 23.4 bundle: replace its 38 impossible rows too, and hold both with a test

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Run_Marvin_Protonations: gate every row on the invariant as it is written

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Document the invariant: README, per-bundle sources.yaml notes, run report

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8a98a54

Commits on Sep 25, 2026

Consume exactly one protonation bundle per source in the structure pick

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Regenerate the structure picks from the repaired 26.1 bundle

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Regenerate the compound records from the new picks

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Refresh pipeline: run the rebalance step, and refresh embedded charges with formulas

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Refresh the reactions against the regenerated compound records

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Run report and README: what the rollout exposed, and the class the invariant cannot see

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Take a compound's formula and charge from the SMILE row when its InChI is the more fragmented

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Regenerate the picks and records with the fragment-count rule

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Refresh the reactions against the re-picked records

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1ad34ad
Annotate post-2020 reactions with pathways; port the step that was lost

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254c1eb