commKinetics updates

freiburgermsu · Sep 18, 2024 · c485552 · c485552
1 parent d198219
commit c485552
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/modelseedpy/core/msmodelutl.py b/modelseedpy/core/msmodelutl.py
@@ -625,7 +625,7 @@ def add_ms_reaction(self, rxn_dict, msdb_path=None, msdb_object=None, comp_trans
         return output
 
     def create_constraint(self, constraint, coef=None, sloppy=False, printing=False):
-        if printing:   print(coef)
+        # if printing:   print(coef)
         self.model.add_cons_vars(constraint, sloppy=sloppy)
         self.model.solver.update()
         if coef:   constraint.set_linear_coefficients(coef)

diff --git a/modelseedpy/fbapkg/commkineticpkg.py b/modelseedpy/fbapkg/commkineticpkg.py
@@ -11,7 +11,7 @@ class CommKineticPkg(BaseFBAPkg):
     def __init__(self, model):
         BaseFBAPkg.__init__(self, model, "community kinetics", {}, {"commKin": "string"})
 
-    def build_package(self, kinetic_coef, community_model, probs=None):
+    def build_package(self, kinetic_coef, community_model, probs={}):
         self.validate_parameters({}, [], {"kinetic_coef": kinetic_coef, "community": community_model})
         for species in self.parameters["community"].members:
             if species.id+"_commKin" in self.model.constraints:
@@ -25,6 +25,5 @@ def build_constraint(self, species, probs):
         for rxn in self.model.reactions:
             rxnIndex = int(FBAHelper.rxn_compartment(rxn)[1:])
             if (rxnIndex == species.index and rxn != species.primary_biomass):
-                val = 1 if not isinstance(probs, dict) else probs.get(rxn.id, 1)
-                coef[rxn.forward_variable] = coef[rxn.reverse_variable] = val
+                coef[rxn.forward_variable] = coef[rxn.reverse_variable] = probs.get(rxn.id, 1)
         return BaseFBAPkg.build_constraint(self, "commKin", None, 0, coef, species.id)