Migrate parser to BRENDA 2026 JSON format#14
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BRENDA now distributes the database as a structured JSON document (schema 2.0.0) instead of the legacy flat text file. Reimplement BRENDA/Reaction to parse the JSON while preserving the public API, and surface the newly available structure (UniProt/GenBank accessions, structured citations with PMIDs, reversibility, synonyms, etc.). - parser.py: JSON-based BRENDA/Reaction; loader accepts .json/.json.gz/.json.tar.gz - constants.py: map fields to JSON schema names; add DATA_FIELDS - tests: re-baseline against committed tests/fixtures/brenda_sample.json - toolchain: Python ^3.10, numpy>=1.24, pandas>=1.5, drop importlib-metadata, bump to 0.1.0, refresh CI matrix (3.10-3.12) - docs: README, examples notebook, JOSS paper, CITATION.cff Behavior changes: Reaction(...) takes the per-EC dict (not text); Reaction.name is verbatim (no more str.capitalize()); BRENDA.fields describes JSON field names; Reaction.references returns citation strings (structured records via the new .bibliography). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
BRENDA's JSON still embeds legacy annotations inside reaction-string
values. Splitting reaction sides on a bare "+" dropped ion charges
(H+ -> H, NAD+ -> NAD), and |...| pipe comments and <ref> tags leaked
into compound names.
- add _clean_reaction_string(): strips |...| comments, {...} reversibility
and numeric <n,n> reference tags, preserving chemical notation such as
glycosidic "(1->4)" bonds and polymer subscripts ([...]n+m)
- split reaction sides on " + " so ionic charges and polymer "+" stay
attached to the compound name (fixes filter_by_substrate/product/compound
for ions, e.g. "NAD+")
- fold substrates_products pipe comments into `comment` instead of
discarding them
Re-addresses the parsing issues reported in #13 against the JSON parser
(ion-charge loss and |...| comment leakage). The parentheses issue (#12)
is already handled by the structured JSON `comment` field.
Co-authored-by: Clark Pohl <clarklettuce@gmail.com>
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This was referenced Jun 14, 2026
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BRENDA now distributes the database as a structured JSON document (schema 2.0.0) instead of the legacy flat text file. Reimplement BRENDA/Reaction to parse the JSON while preserving the public API, and surface the newly available structure (UniProt/GenBank accessions, structured citations with PMIDs, reversibility, synonyms, etc.).
Behavior changes: Reaction(...) takes the per-EC dict (not text); Reaction.name is verbatim (no more str.capitalize()); BRENDA.fields describes JSON field names; Reaction.references returns citation strings (structured records via the new .bibliography).