Additive per-source thermodynamic descriptions (reaction free energies + compound pKas)

[freiburgermsu]

Summary

Records every thermodynamic / pKa source side-by-side instead of collapsing them into a single value. Purely additive — no canonical free-energy or served-pKa value changes, and no TSV changes (thermodynamics and pkas are JSON-only fields).

Reaction free energies — thermodynamics dict

Each method now carries an [energy, error, operator] triple. The operator (>, <, =, ?) is that estimate's own thermodynamic direction, computed with the same heuristic as the canonical reversibility applied to that method's dG:

"thermodynamics": {
"Group contribution": [4.15, 1.22, "="],
"eQuilibrator": [-3.46, 0.05, ">"],
"dGPredictor": [-3.82, 0.02, ">"]
}

• dGPredictor (Wang et al. 2021; predictions already staged under Biochemistry/Thermodynamics/dGPredictor/, kJ→kcal /4.184) is recorded additively for every reaction it predicts (27,715), next to GC/eQ. It does not alter the canonical deltag/deltagerr/reversibility.
• Estimate_Reaction_Reversibility.py is refactored to expose a reusable reversibility_from_energy(). The dev coercion fix (float(rxn_dg)) is preserved, and the refactor reproduces dev's reversibility output exactly on all 56,012 reactions (validated). New Update_Reaction_dGPredictor_Energies.py (additive-only) and Add_Reaction_Thermodynamics_Operators.py; the GC/eQ writers attach the operator.

Compound pKas — pkas dict

New per-tool pkas dict keyed by predicting tool, each {pKa, pKb} in the existing <microstate>:<atom>:<value> encoding, next to the served pka/pkb:

"pkas": {
"Marvin": {"pKa": "1:14:12.60;1:22:3.33;...", "pKb": "1:9:-3.03;1:14:-3.85;..."},
"MolGpKa": {"pKa": "1:14:10.12;1:29:0.98;...", "pKb": "1:6:3.66;1:9:3.42;..."}
}

• Marvin = the cascade-winning per-database Marvin value; MolGpKa = the OPAM2/MolGpKa prediction (new source file Biochemistry/Structures/ModelSEED/pkas/opam2_molgpka.tsv, 22,399 compounds).
• The served pka/pkb are unchanged (the existing cascade-picked Marvin value).
• New Scripts/Structures/Add_Compound_pKa_Sources.py builds the dict (idempotent, never touches served pka/pkb); added to the manifest cascade as the AddPkaSources stage.

Data changed

• 27,715 reactions gained a dGPredictor record; 75,497 GC/eQ records gained an operator.
• 35,632 compounds gained a Marvin record; 22,395 a MolGpKa record.
• Verified: zero changes to canonical deltag/deltagerr/reversibility/notes, served pka/pkb, any other field, or any .tsv.

Docs updated in Scripts/Thermodynamics/README.md and Biochemistry/Structures/sources.yaml.

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