MSprobability and CommKinetics updates

freiburgermsu · Mar 14, 2024 · fdaf0a2 · fdaf0a2
1 parent 04e940d
commit fdaf0a2
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/modelseedpy/core/msprobability.py b/modelseedpy/core/msprobability.py
@@ -1,5 +1,5 @@
 from cobrakbase.core.kbasefba.fbamodel_from_cobra import CobraModelConverter
-from modelseedpy.fbapkg.mspackagemanager import MSPackageManager
+# from modelseedpy.fbapkg.mspackagemanager import MSPackageManager
 from modelseedpy.community.mscommunity import MSCommunity
 from cobrakbase.core.kbasefba.fbamodel import FBAModel
 from cobra.io import write_sbml_model, read_sbml_model
@@ -128,9 +128,9 @@ def prFBA(model_s_, environment=None, abundances=None, min_prob=0.01, prob_exp=1
         elepkg = ElementUptakePkg(mdlUtil.model)  ;  elepkg.build_package({"C": 100})
         ## the total flux through the members proportional to their relative abundances
         if not commkinetics and len(model_s_) > 1:
-            pkgmgr = MSPackageManager.get_pkg_mgr(mdlUtil.model)
+            # pkgmgr = MSPackageManager.get_pkg_mgr(mdlUtil.model)
             MSCommObj = MSCommunity(mdlUtil.model, model_s_)
-            pkgmgr.getpkg("CommKineticPkg").build_package(kinetics_coef, MSCommObj)
+            # pkgmgr.getpkg("CommKineticPkg").build_package(kinetics_coef, MSCommObj)
 
         # constrain the model to 95% of the optimum growth
         maxBioSol = mdlUtil.model.slim_optimize()

diff --git a/modelseedpy/fbapkg/commkineticpkg.py b/modelseedpy/fbapkg/commkineticpkg.py
@@ -7,6 +7,7 @@
 from modelseedpy.core.fbahelper import FBAHelper
 
 # Base class for FBA packages
+# TODO This code may need to refactored to not require an MSCommunity object, which is circular logic
 class CommKineticPkg(BaseFBAPkg):
     def __init__(self, model):
         BaseFBAPkg.__init__(self, model, "community kinetics", {}, {"commkin": "string"})
@@ -20,6 +21,5 @@ def build_constraint(self, member):
         bioRXN = member.primary_biomass
         coef = {bioRXN.forward_variable: -self.parameters["kinetic_coef"], bioRXN.reverse_variable: self.parameters["kinetic_coef"]}
         for reaction in member.reactions:
-            if int(FBAHelper.rxn_compartment(reaction)[1:]) == member.index and reaction != bioRXN:
-                coef[reaction.forward_variable] = coef[reaction.reverse_variable] = 1
+            if reaction != bioRXN:   coef[reaction.forward_variable] = coef[reaction.reverse_variable] = 1
         return BaseFBAPkg.build_constraint(self, "commkin", None, 0, coef, "Species" + str(member.index))