GECKO 3.2.1 #383
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GECKO 3.2.1 #383
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…onstrainFluxData (#382) * fix: getECfromDatabase correct input parameter doc * feat: makeEcModel error if none of proteins match * fix: getStandardKcat not remove if real enzyme * style: various * todo: refactor fuzzyKcatMatching to use regexprep * fix: calculateFfactor handle protData multi conds * fix getStandardKcat * feat: setKcatForReactions allows multiple kcat as input * feat: reportEnzymeUsage if enzyme cat. more rxns * chore: updateGECKOdoc * fix: reportEnzymeUsage correct percUsage * fix: constrainFluxData (-)1000 constraints * fix: ecFVA correct swapped rev fluxes * fix: reportEnzymeUsage highUsage split isozymes * refactor: fuzzyKcatMatching use regexprep * fix: plotEcFVA cdfplot and only plot non-zero rxns * feat: constrainEnzConcs can remove enzConstraints * chore: rerun tutorials * fix: getStandardKcat for light ecModels * fix: constrainEnzConcs remove enz constraints
edkerk
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getStandardKcat.mremoved enzymes when it was run on a model already containing standard kcat valuesecFVAwill swapminandmaxvalues the reaction directionality was swapped when mapping from ec- to conventional modelplotEcFVAwill use its owncdfplotfunction, to avoid dependency on MATLAB Statistics and Machine Learning Toolbox. Blocked reactions are excluded from the graph.full_ecModelshows minor differences, also due to code changes introduced by GECKO 3.2.0can handleprotData` with multiple conditions (in which case, averages over all conditions are taken)setKcatForReactionsallows multiple kcat values as input, allowing to set kcat of multiple reactions at the same timereportEnzymeUsagewill report both the summed usage of isoenzymes, as well as the individual usage of the separate reactions.topUsageandhighCapUsageoutputs columns are harmonizedconstrainFluxDataif a provided constraint is either -1000 or 1000, lower and upper bound will be constraint to either uptake or excretion only, irrespective of what option is given as thelooseStrictFluxparameterconstrainEnzConcscan also remove enzyme concentration constraintsfuzzyKcatMatchingto avoid warnings "Colon operands must be real scalars" in recent MATLAB versionsInstructions on merging this PR:
developas target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved with a merge commit.