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get_enzyme_bottlenecks ranks by the re-solved change of the objective - #77
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The order no longer depends on the shadow price, which depends on the basis at a degenerate optimum. Enzymes at their bound are solved again with the bound raised by fold_change; multiple_active marks rows where another capacity constraint is active.
…and requires a fold_change above 1
# Conflicts: # CHANGELOG.md
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Enzymes at their usage bound are solved again with the bound raised by
fold_change(default 2, greater than 1) and ranked by the improvement of the objective,objective_gain; other enzymes have gain 0 without a solve. Ties keep the order ofmodel.enzymes.shadow_pricestays as a reference column and does not affect the order, because at a degenerate optimum it depends on the basis.multiple_activemarks an enzyme when another capacity constraint, an enzyme at its bound or the protein pool, is active at the same optimum.df.attrsholdsn_resolvedandactive_constraints. When no enzyme is at its usage bound, a warning says that no single enzyme limits the objective.The columns are
gene, objective_gain, shadow_price, flux, cap_usage, upper_bound, multiple_active; callers that read the table by position must use the column names.Parity: CompMetEng/raven-gecko-parity#117.