Make configurable change to define reaction flux bounds in metabolism.py

ecoli/processes/metabolism.py

@@ -95,6 +95,7 @@ class Metabolism(Step):
         "linked_metabolites": None,
         "aa_exchange_names": [],
         "removed_aa_uptake": [],
+        "set_reaction_bounds": {},  # In form: {RXN_ID:[lb,ub]}
         "seed": 0,
         # TODO: For testing, remove later (perhaps after modifying sim data)
         "reduce_murein_objective": False,
@@ -532,6 +533,27 @@ def next_update(self, timestep, states):
             catalyst_counts, counts_to_molar, coefficient, translation_gtp
         )
 
+        # Set reaction limits from config options
+        config_reaction_bounds = self.parameters.get("set_reaction_bounds", {})
+        for rxn, bounds in config_reaction_bounds.items():
+            if rxn not in self.fba_reaction_ids:
+                raise ValueError(
+                    f"set_reaction_bounds: reaction '{rxn}' not found in FBA reaction IDs"
+                )
+            try:
+                lower_bound, upper_bound = bounds
+            except (TypeError, ValueError) as e:
+                raise ValueError(
+                    f"set_reaction_bounds for '{rxn}' must be a 2-item sequence [lower, upper], got: {bounds!r}"
+                ) from e
+            if lower_bound > upper_bound:
+                raise ValueError(
+                    f"set_reaction_bounds for '{rxn}' has lower_bound > upper_bound ({lower_bound} > {upper_bound})"
+                )
+            self.model.fba.setReactionFluxBounds(
+                rxn, lowerBounds=lower_bound, upperBounds=upper_bound
+            )
+
         # Constrain reactions based on targets
         targets, upper_targets, lower_targets = self.model.set_reaction_targets(
             kinetic_enzyme_counts,