Promote per-source thermodynamics to canonical deltag (+ retrained dGPredictor-ModelSEED source) - #265
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samseaver merged 2 commits intoAug 4, 2026
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…urce Records the dGPredictor group-contribution model retrained on the ModelSEED compound structures as its own per-method entry, "dGPredictor-ModelSEED", in each reaction's `thermodynamics` dict. Purely additive: it sits next to the Group contribution / eQuilibrator / (original KEGG-based) dGPredictor records, and the original "dGPredictor" entry is left untouched. The canonical deltag / deltagerr / reversibility are not changed, and no .tsv or compound files change. - New staged predictions: Biochemistry/Thermodynamics/dGPredictor/ modelseed_retrained_dG.json (31,924 reactions, kJ/mol). - New writer: Scripts/Thermodynamics/Update_Reaction_dGPredictor_ModelSEED_ Energies.py (kJ->kcal /4.184; operator via reversibility_from_energy). - 31,924 reactions gain a dGPredictor-ModelSEED record (incl. ~11,400 the original KEGG-based dGPredictor could not reach); 24,088 reactions unchanged. - Verified: every modified reaction differs from dev ONLY by the added dGPredictor-ModelSEED key; added values equal dG_mean/4.184; the writer is idempotent. - Docs: sources.yaml, Scripts/Thermodynamics/README.md, Rerun_Thermodynamics.sh. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…141 reactions) After the additive-thermodynamics refactor, the Update_Reaction_*_Energies.py scripts write only into each reaction's additive `thermodynamics` dict and no longer populate the canonical top-level deltag/deltagerr. As a result 14,141 non-EMPTY reactions carried a perfectly good computed energy in `thermodynamics` while their canonical deltag stayed the 10000000 sentinel (reversibility "?"), so they read as thermodynamically undefined despite the value already existing. New Scripts/Thermodynamics/Promote_Reaction_Thermodynamics_to_Canonical.py re-aggregates those existing per-source estimates into the canonical fields. It is pure re-aggregation -- no new estimation, no external dependencies: - Only reactions whose canonical deltag is missing are touched; existing canonical values are never overwritten. - Selection: prefer the mechanistic/measurement-anchored tier (eQuilibrator, then Group contribution) over the ML tier (dGPredictor-ModelSEED, dGPredictor); WITHIN the chosen tier take the lowest-uncertainty estimate. The within-tier lowest-error rule prevents a wildly-uncertain ML outlier (e.g. -100 +/- 71 kcal/mol) from being promoted over a tight estimate (-8.6 +/- 0.04). - Guards reject implausible magnitudes (|dG| > 1000 kcal/mol) and useless uncertainties (> 100 kcal/mol), leaving those reactions undefined rather than promoting garbage. - deltagerr is set from the chosen source and reversibility is set to that estimate's own direction operator (same heuristic as Estimate_Reaction_ Reversibility, already stored alongside each per-source energy). Promoted 14,141 reactions: Group contribution 1,474; dGPredictor 8,635; dGPredictor-ModelSEED 4,032. Verified: every promoted deltag equals one of the reaction's stored per-source energies; zero pre-existing canonical values, thermodynamics dicts, or other fields changed. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Re-ran Scripts/Biochemistry/Reprint_Biochemistry.py to bring the equation and definition strings in sync with the newly-promoted reversibility values from PR #265. Freiburgermsu's promotion populated the reversibility field for 14,141 reactions but did not re-render the equation and definition strings, which encode the same reversibility operator in human-readable form. This commit does that re-rendering. Zero data changes beyond the string re-rendering (deltag, deltagerr, compound_ids, stoichiometry, and all other fields unchanged). Also resolves the 34 reaction .tsv conflicts that arose during the PR #265 merge (both dev and freiburgermsu's branch had independently regenerated TSVs from their respective JSONs; regeneration from the merged JSONs is the correct post-merge state). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Fixes eQuilibrator retrieval scripts for equilibrator_api 0.6.x (API drift; module-level ccache singleton removed, ComponentContribution no longer takes reaction conditions as constructor kwargs). Re-runs the pipeline against updated ModelSEED structures. Coverage expansion in the pre-computed source tables: - MetaNetX_Compound_Energies.tbl: 20,828 -> 31,219 rows (+10,391 compounds) - MetaNetX_Reaction_Energies.tbl: 22,441 -> 27,022 rows (+4,581 reactions) - 16,412 reactions re-tagged EQP -> EQC / EQC -> EQP in notes to reflect the new per-reagent coverage. Andrew's commit explicitly notes: only the eQuilibrator energy tables and reaction notes change here; canonical deltag/deltagerr/reversibility and the additive thermodynamics dicts are untouched. Propagation into served compound_*.json and reaction_*.json records is a separate step, run in follow-up commits. Directly fills the compound-level coverage gap identified during audit of the post-#264/#265 dev state (30,479 non-R structured compounds, only 22,616 with any deltag before this branch). Conflict resolution: 61 reaction .tsv files conflicted between dev's TSVs and freiburgermsu's TSVs. Resolved by taking dev's side then regenerating all TSVs from the merged JSONs via Reprint_Biochemistry.py in the next commit. Co-Authored-By: Andrew Freiburger <freiburgermsu@aol.com> # Conflicts: # Biochemistry/reaction_00.tsv # Biochemistry/reaction_01.tsv # Biochemistry/reaction_02.tsv # Biochemistry/reaction_03.tsv # Biochemistry/reaction_04.tsv # Biochemistry/reaction_05.tsv # Biochemistry/reaction_06.tsv # Biochemistry/reaction_07.tsv # Biochemistry/reaction_08.tsv # Biochemistry/reaction_09.tsv # Biochemistry/reaction_10.tsv # Biochemistry/reaction_11.tsv # Biochemistry/reaction_12.tsv # Biochemistry/reaction_13.tsv # Biochemistry/reaction_14.tsv # Biochemistry/reaction_15.tsv # Biochemistry/reaction_16.tsv # Biochemistry/reaction_17.tsv # Biochemistry/reaction_18.tsv # Biochemistry/reaction_19.tsv # Biochemistry/reaction_20.tsv # Biochemistry/reaction_21.tsv # Biochemistry/reaction_22.tsv # Biochemistry/reaction_23.tsv # Biochemistry/reaction_24.tsv # Biochemistry/reaction_25.tsv # Biochemistry/reaction_26.tsv # Biochemistry/reaction_27.tsv # Biochemistry/reaction_28.tsv # Biochemistry/reaction_29.tsv # Biochemistry/reaction_30.tsv # Biochemistry/reaction_31.tsv # Biochemistry/reaction_32.tsv # Biochemistry/reaction_33.tsv # Biochemistry/reaction_34.tsv # Biochemistry/reaction_35.tsv # Biochemistry/reaction_36.tsv # Biochemistry/reaction_37.tsv # Biochemistry/reaction_38.tsv # Biochemistry/reaction_39.tsv # Biochemistry/reaction_40.tsv # Biochemistry/reaction_41.tsv # Biochemistry/reaction_42.tsv # Biochemistry/reaction_43.tsv # Biochemistry/reaction_44.tsv # Biochemistry/reaction_45.tsv # Biochemistry/reaction_46.tsv # Biochemistry/reaction_47.tsv # Biochemistry/reaction_48.tsv # Biochemistry/reaction_49.tsv # Biochemistry/reaction_50.tsv # Biochemistry/reaction_51.tsv # Biochemistry/reaction_52.tsv # Biochemistry/reaction_53.tsv # Biochemistry/reaction_54.tsv # Biochemistry/reaction_55.tsv # Biochemistry/reaction_56.tsv # Biochemistry/reaction_57.tsv # Biochemistry/reaction_58.tsv # Biochemistry/reaction_59.tsv # Biochemistry/reaction_60.tsv
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Two sub-steps run in sequence: 1. Update_Reaction_eQuilibrator_Energies.py Folds the freshly-computed eQuilibrator reaction values (from the +4,581-reaction rerun in Andrew's branch, merged at c1149b7) into each reaction's additive 'thermodynamics' dict as an 'eQuilibrator' entry. 2. Promote_Reaction_Thermodynamics_to_Canonical.py Re-runs the promotion policy from PR #265 against the now-updated thermodynamics dicts. Promotes an additional 150 reactions to canonical deltag (all from eQuilibrator; the previous run had already caught the promotable candidates from GC + dGPredictor). Coverage state after this commit: Total reactions: 56,012 Per-source entries: eQuilibrator (post-rerun): 25,028 Group contribution: 55,999 dGPredictor (KEGG-trained): 27,715 dGPredictor-ModelSEED (retrained): 31,924 Canonical deltag: 39,051 -> 39,201 (+150) Unpromotable: 16,801 (no source estimate, or all fail the >100 kcal/mol uncertainty guard) Reaction JSONs+TSVs regenerated via Reprint_Biochemistry.py for consistency (equation/definition strings reflect any updated reversibility operators). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
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Summary
Gives 14,141 reactions a canonical free-energy value (
deltag/deltagerr/reversibility) that they were missing — purely by re-aggregating estimates that already exist in the additivethermodynamicsdict, plus the retrained dGPredictor source that supplies some of them.Background: the promotion gap
After the additive-thermodynamics refactor, the
Update_Reaction_*_Energies.pyscripts write only into each reaction's additivethermodynamicsdict and no longer populate the canonical top-leveldeltag/deltagerr. As a result thousands of reactions carried a perfectly good computed energy inthermodynamicswhile their canonicaldeltagstayed the10000000sentinel (andreversibility"?"), so they read as thermodynamically undefined despite the value already existing.What this PR does
Two commits:
dGPredictor-ModelSEEDsource (existing additive work) — the dGPredictor group-contribution model retrained on ModelSEED structures, recorded as its own per-method entry inthermodynamics. Additive; supplies energies for reactions the other sources miss.Promotion — new
Scripts/Thermodynamics/Promote_Reaction_Thermodynamics_to_Canonical.pyre-aggregates the stored per-source estimates into the canonical fields. Pure re-aggregation: no new estimation, no external dependencies.deltagare touched; existing canonical values are never overwritten.eQuilibrator→Group contribution) over the ML tier (dGPredictor-ModelSEED,dGPredictor); within the chosen tier take the lowest-uncertainty estimate. The within-tier lowest-error rule stops a wildly-uncertain ML outlier (e.g.-100 ± 71kcal/mol) being promoted over a tight estimate (-8.6 ± 0.04).|dG| > 1000) and useless uncertainties (> 100kcal/mol), leaving those undefined rather than promoting garbage.reversibilityis set to the chosen estimate's own direction operator (same heuristic asEstimate_Reaction_Reversibility.py, already stored with each per-source energy).Result
14,141 reactions promoted: Group contribution 1,474 · dGPredictor 8,635 · dGPredictor-ModelSEED 4,032.
Verified: every promoted
deltagequals one of that reaction's stored per-source energies; zero pre-existing canonical values,thermodynamicsdicts, or other fields changed. (.tsvfiles update becausedeltag/deltagerr/reversibilityare TSV columns.)The source-precedence policy is a single editable
TIERSconstant; ~732 reactions have >50 kcal/mol cross-source disagreement and are worth a curator spot-check (the policy resolves them by tier + lowest error, not averaging).🤖 Generated with Claude Code