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fuzzyKcatMatching: refactoring of BRENDA-based approach

Open edkerk opened this issue 3 years ago • 0 comments
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Description of the new feature:

Instead of having GECKO's fuzzy matching approach directly modify the stoichiometric coefficients in the model, let it populate the model.kcat structure introduced in #156.

  • [ ] Use the model.ec.kcat structure as input for matchKcats, instead of the output from getEnzymeCodes
  • [ ] Instead of matchKcats always doing fuzzy matching, also have an option to only report (near-)precise matches.
  • [ ] Do not have readKcatData to directly modify the stoichiometric coefficients, but instead write kcat values into the model.ec.kcat structure. Instead, applyKcatConstraints can modify the S-matrix for selected reactions (with updateRxns flag).

edkerk avatar May 25 '22 21:05 edkerk