Sync fbapkg/commkineticpkg.py from freiburgermsu fork

modelseedpy/fbapkg/commkineticpkg.py

@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+
+import logging
+from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
+from modelseedpy.core.fbahelper import FBAHelper
+
+# Base class for FBA packages
+class CommKineticPkg(BaseFBAPkg):
+    def __init__(self, model):
+        BaseFBAPkg.__init__(self, model, "community kinetics", {}, {"commKin": "string"})
+
+    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:
+                print(f"Removing {species.id+'_commKin'} from {self.model.id}")
+                self.model.remove_cons_vars(self.model.constraints[species.id+"_commKin"])
+            self.build_constraint(species, probs)
+
+    def build_constraint(self, species, probs):
+        coef = {species.primary_biomass.forward_variable: -self.parameters["kinetic_coef"],
+                species.primary_biomass.reverse_variable: self.parameters["kinetic_coef"]}
+        for rxn in self.model.reactions:
+            rxnIndex = int(FBAHelper.rxn_compartment(rxn)[1:])
+            if (rxnIndex == species.index and rxn != species.primary_biomass):
+                coef[rxn.forward_variable] = coef[rxn.reverse_variable] = probs.get(rxn.id, 1)
+        return BaseFBAPkg.build_constraint(self, "commKin", None, 0, coef, species.id)