Keep gathered kcats as kcat source files, one per source

.gitattributes

@@ -13,3 +13,6 @@
 *.txt   text eol=lf
 *.xml   text eol=lf
 *.md    text eol=lf
+
+# A fixture that must keep its byte-order mark and CRLF line endings.
+tests/data/kcatSourceFixture.tsv -text

docs/migrating_from_gecko_matlab.md

@@ -247,6 +247,11 @@ Each row maps a MATLAB function to its geckopy equivalent. The
 | `fetchOpenKineticsPredictor`        | `fetch_open_kinetics_predictor`      | **`[3→4]`** New REST-based fetch (replaced `readOpenKineticsPredictorOutput`); per-row `kcatSource` reports actual provenance (CataPro / BRENDA / Sabio-RK).                                                                  |
 | `writeOpenKineticsPredictorInput`   | *(removed)*                          | **`[3→4]`** Replaced by `submit_open_kinetics_predictor`.                                                                                                                                                                      |
 | `readOpenKineticsPredictorOutput`   | *(removed)*                          | **`[3→4]`** Replaced by `fetch_open_kinetics_predictor`.                                                                                                                                                                       |
+| `kcatsFromBrenda`                   | `kcats_from_brenda`                  | Fuzzy BRENDA matching, kept as `data/kcats/brenda.tsv`. Loads the BRENDA data and KEGG distances from the adapter unless passed in. |
+| `kcatsFromDLKcat`                   | `kcats_from_dlkcat`                  | DLKcat (run in Docker with `run=True`, or an earlier output), kept as `data/kcats/dlkcat.tsv`. |
+| `kcatsFromOKP`                      | `kcats_from_okp`                     | One OpenKineticsPredictor method, kept as `data/kcats/okp_<method>.tsv`; submits a job when there is none, writes the file once it is done. Returns `(kcat_list, done)`. |
+| `saveKcatSource`, `readKcatSource`, `loadKcatSource` | `save_kcat_source`, `read_kcat_source`, `load_kcat_source` | Kcat source files: one per source, keyed by conventional reaction and enzyme set, the same file format in both tools. `load_kcat_source` maps a file to the current model and reports rows that fit no reaction. |
+| `getEcRxnKeys`                      | `ec_rxn_keys`                        | Conventional reaction and enzyme set per `ec.rxns` entry. |
 
 ### 5.3 Get enzyme data (`src/geckomat/get_enzyme_data`)
 

src/geckopy/__init__.py

@@ -78,11 +78,17 @@
     fetch_open_kinetics_predictor,
     fuzzy_kcat_matching,
     get_standard_kcat,  # deprecated; alias of assign_standard_kcat
+    kcats_from_brenda,
+    kcats_from_dlkcat,
+    kcats_from_okp,
+    load_kcat_source,
     merge_dlkcat_and_fuzzy_kcats,  # deprecated; alias of merge_kcats
     merge_kcats,
     read_dlkcat_output,
+    read_kcat_source,
     remove_standard_kcat,
     run_dlkcat,
+    save_kcat_source,
     select_kcat_value,  # deprecated; alias of apply_kcat_list
     submit_open_kinetics_predictor,
     write_dlkcat_input,
@@ -186,11 +192,17 @@
     "assign_standard_kcat",
     "fetch_open_kinetics_predictor",
     "fuzzy_kcat_matching",
+    "kcats_from_brenda",
+    "kcats_from_dlkcat",
+    "kcats_from_okp",
+    "load_kcat_source",
     "merge_dlkcat_and_fuzzy_kcats",  # deprecated; alias of merge_kcats
     "merge_kcats",
     "read_dlkcat_output",
+    "read_kcat_source",
     "remove_standard_kcat",
     "run_dlkcat",
+    "save_kcat_source",
     "submit_open_kinetics_predictor",
     "write_dlkcat_input",
     # get_enzyme_data

src/geckopy/gather_kcats/__init__.py

@@ -3,6 +3,8 @@
 Mirrors GECKO MATLAB's `src/geckomat/gather_kcats/` directory.
 """
 from .fuzzy_kcat_matching import fuzzy_kcat_matching
+from .kcat_sources import ec_rxn_keys, load_kcat_source, read_kcat_source, save_kcat_source
+from .kcats_from import kcats_from_brenda, kcats_from_dlkcat, kcats_from_okp
 from .get_standard_kcat import assign_standard_kcat, get_standard_kcat
 from .merge_dlkcat_and_fuzzy_kcats import merge_dlkcat_and_fuzzy_kcats
 from .merge_kcats import merge_kcats, normalize_source
@@ -27,17 +29,24 @@
     "OKPError",
     "apply_kcat_list",
     "assign_standard_kcat",
+    "ec_rxn_keys",
     "extract_enzyme_substrate_pairs",
     "fetch_open_kinetics_predictor",
     "format_kcat_source",
     "fuzzy_kcat_matching",
     "get_standard_kcat",  # deprecated; alias of assign_standard_kcat
+    "kcats_from_brenda",
+    "kcats_from_dlkcat",
+    "kcats_from_okp",
+    "load_kcat_source",
     "merge_dlkcat_and_fuzzy_kcats",  # deprecated; use merge_kcats
     "merge_kcats",
     "normalize_source",
+    "read_kcat_source",
     "read_dlkcat_output",
     "remove_standard_kcat",
     "run_dlkcat",
+    "save_kcat_source",
     "select_kcat_value",  # deprecated; alias of apply_kcat_list
     "submit_open_kinetics_predictor",
     "write_dlkcat_input",

src/geckopy/gather_kcats/fuzzy_kcat_matching/__init__.py

@@ -36,6 +36,7 @@
 from ._organism import filter_by_organism, resolve_organism_index
 
 if TYPE_CHECKING:
+    from ...adapter import ModelAdapter
     from ...databases import BrendaData, PhylDist
     from ...ec_model.ec_model import EcModel
 
@@ -81,6 +82,7 @@ def fuzzy_kcat_matching(
     ec_rxns: Optional[Iterable[str]] = None,
     force_wildcard_level: int = 0,
     aggregate: Optional[str] = None,
+    adapter: Optional["ModelAdapter"] = None,
 ) -> pd.DataFrame:
     """Match each ec reaction to BRENDA kcat data with progressive
     relaxation of EC, substrate, and organism specificity.
@@ -161,6 +163,9 @@ def fuzzy_kcat_matching(
         across whichever rows survive the EC + organism + substrate
         gates. See ``docs/kcat_aggregation.md`` for the empirical
         rationale.
+    adapter
+        Model adapter for ``org_name`` and the aggregation default
+        (default: ``model.adapter``).
 
     Returns
     -------
@@ -182,7 +187,7 @@ def fuzzy_kcat_matching(
     """
     from ...adapter import resolve_adapter
     adapter = resolve_adapter(
-        model,
+        model, adapter,
         purpose="fuzzy_kcat_matching reads params.org_name from the adapter",
     )
     if force_wildcard_level < 0: