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Assign kcats from the kcat source files, as model_adapter.toml sets - #9
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Gathered kcats are written to data/kcats/<source>.tsv in the project, keyed by conventional reaction and enzyme set rather than model.ec.rxns, so a file stays valid when the ecModel is rebuilt and applies to full and light models alike. geckopy reads and writes the same files. - kcatsFromBrenda, kcatsFromDLKcat and kcatsFromOKP gather one source each, with that source's own options, and write its file. OKP keeps a job and a result per method, and only uses a stored result of the current job. - saveKcatSource writes any kcat list; readKcatSource reads a file; loadKcatSource maps a file to a model and reports rows with an invalid kcat, rows that fit no reaction, and rows that match only part of an enzyme set. - getEcRxnKeys gives the conventional reaction and enzyme set of every model.ec reaction. - fetchOpenKineticsPredictor takes the file to store the result in. Original-commit: SysBioChalmers/GECKO@f3a696c
…t-assignment Original-commit: SysBioChalmers/GECKO@ed138e1
collectKcats decides one kcat per reaction from the files in data/kcats, in the stages of [kcat_assignment] (a preset, or [[kcat_assignment.stage]] tables), without changing the model, and writes output/<model id>_kcatDecisions.tsv. assignKcats applies the decisions and the kcat constraints. updateKcatSources gathers the source files the configuration needs that are missing, or outdated against [kcat_sources.<name>]. The default preset, gecko_median, orders custom kcats, the BRENDA median of matches without EC wildcards at origins 1 to 4, DLKcat, then the other BRENDA matches. gecko_classic keeps the GECKO 3 order with the BRENDA maximum; the full_ecModel tutorial uses it and gives the same model as before.
Unit test results61 tests 61 ✅ 9s ⏱️ Results for commit 4dc7292. ♻️ This comment has been updated with latest results. |
…iles # Conflicts: # test/VerificationMatrix.tsv
loadKcatSource reads the file itself and returns the header lines and the rows as read in report.header and report.records; readKcatSource is gone. The helpers of src/gather_kcats/private are local functions of the functions that use them. kcatsFrom<Source> no longer check the file name before gathering; saveKcatSource does when it writes.
…t/kcat-assignment # Conflicts: # test/VerificationMatrix.tsv
# Conflicts: # test/VerificationMatrix.tsv
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Kcats are assigned from the kcat source files in
data/kcats(#3), in an order thatmodel_adapter.tomlsets. geckopy has the same functions and settings (CompMetEng/geckopy#66). This is step K2 of the plan in CompMetEng/raven-gecko-parity#134.Builds on #3 (kcat source files); the diff shows its changes until it is merged.
Functions
collectKcatsoutput/<model id>_kcatDecisions.tsv(stage, source, kcat, number of values and their spread per reaction)assignKcatscollectKcats, then writesec.kcatandec.sourceand applies the kcat constraints. ReplacesmergeKcats→assignKcatValues→applyCustomKcats→getKcatAcrossIsozymes→getStandardKcat→applyKcatConstraints, which stay callableupdateKcatSourceskcatsFromBrenda,kcatsFromDLKcat,kcatsFromOKP) when they are missing, or when their header records other settings or another BRENDA release than asked;'dryRun', trueonly reportskcatAssignmentConfig[kcat_assignment]and[kcat_sources.*], with a preset expanded into its stagesConfiguration
mergeKcats). Sources are source file names and the BRENDA tiersdatabase_exact,database_topanddatabase_bottom, which readbrenda.tsv.data/kcats/custom.tsv,data/customKcats.tsvis applied as before.Presets
gecko_median(default)gecko_classicThe order of
gecko_mediancomes from comparing each BRENDA tier with DLKcat on measured kcats hidden from the search: the BRENDA median was as close or closer at every origin without wildcards, and the maximum was further off than the median in every tier. Specific-activity matches could not be compared; they rank below DLKcat because a specific activity converted with a molecular weight from another organism broke kcat tuning in ecYeastGEM (geckopy#58). The figures are in CompMetEng/raven-gecko-parity#134.Tutorial
full_ecModeluseskcatsFromBrenda,kcatsFromDLKcatandassignKcatsfor STEP 18–31, withpreset = "gecko_classic". The ecModel is identical to the one the previous steps gave: 4834ec.rxns, the sameec.kcat,ec.sourceandS.Tests
kcatAssignmentTests(tc0079–tc0083):gecko_classicandgecko_medianagainst the chain of functions they replace,collectKcatsleaving the model unchanged,custom.tsvdeciding first, stages from TOML and their errors, andupdateKcatSourcesgathering missing and outdated files only.