Sync fbapkg/simplethermopkg.py from freiburgermsu fork

modelseedpy/fbapkg/simplethermopkg.py

@@ -1,81 +1,80 @@
-# -*- coding: utf-8 -*-
-
-from __future__ import absolute_import
-import logging
-from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
-from optlang.symbolics import Zero
-import re
-
-# Base class for FBA packages
-class SimpleThermoPkg(BaseFBAPkg):
-    def __init__(self, model):
-        BaseFBAPkg.__init__(
-            self,
-            model,
-            "simple thermo",
-            {"potential": "metabolite", "dgp":"reaction"},
-            {"thermo": "reaction", "dgpc": "reaction"},
-        )
-        self.pkgmgr.addpkgs(["RevBinPkg"])
-
-    def build_package(self, parameters):
-        self.validate_parameters(
-            parameters,
-            [],
-            {
-                "filter": None,
-                "max_potential": 10000,
-                "exclude_reactions": []
-            },
-        )
-        self.pkgmgr.getpkg("RevBinPkg").build_package(self.parameters["filter"])
-        for metabolite in self.model.metabolites:
-            self.build_potential_variable(metabolite)
-        for reaction in self.model.reactions:
-            if reaction.id[:3] not in ["EX_", "SK_", "DM_"] and reaction.id not in self.parameters["exclude_reactions"]:
-                self.build_dgp_variable(reaction)
-                self.build_dgp_constraint(reaction)
-                self.build_fluxcoupling_constraint(reaction)
-
-    def build_potential_variable(self, object):
-        return self.build_variable(
-            "potential",
-            -1*self.parameters["max_potential"],
-            self.parameters["max_potential"],
-            "continuous",
-            object,
-        )
-
-    def build_dgp_variable(self, object):
-        return self.build_variable(
-            "dgp",
-            -1*self.parameters["max_potential"],
-            self.parameters["max_potential"],
-            "continuous",
-            object,
-        )
-
-    def build_dgp_constraint(self, object):
-        # Gibbs: dg = Sum(st(i,j)*p(j))
-        # 0 <= (-1) dgp(i) + Sum(st(i,j)*p(j)) <= 0
-        coef = {}
-        for metabolite in object.metabolites:
-            coef[self.variables["potential"][metabolite.id]] = object.metabolites[
-                metabolite
-            ]
-        coef[self.variables["dgp"][object.id]] = -1
-
-        return self.build_constraint(
-            "dgpc", 0, 0, coef, object
-        )
-
-    def build_fluxcoupling_constraint(self, object):
-        # Gibbs: dg = Sum(st(i,j)*p(j)) 
-        #  0 <= dgp(i) + max_energy_magnitude*revbin(i) <= max_energy_magnitude
-        coef = {}
-        coef[self.variables["dgp"][object.id]] = 1
-        coef[self.pkgmgr.getpkg("RevBinPkg").variables["revbin"][object.id]] = self.parameters["max_potential"]+1
-        # build the constraint
-        return self.build_constraint(
-            "thermo", 0, (self.parameters["max_potential"]+1), coef, object
-        )
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+import logging
+from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
+from optlang.symbolics import Zero
+
+# Base class for FBA packages
+class SimpleThermoPkg(BaseFBAPkg):
+    def __init__(self, model):
+        BaseFBAPkg.__init__(
+            self,
+            model,
+            "simple thermo",
+            {"potential": "metabolite", "dgp":"reaction"},
+            {"thermo": "reaction", "dgpc": "reaction"},
+        )
+        self.pkgmgr.addpkgs(["RevBinPkg"])
+
+    def build_package(self, parameters):
+        self.validate_parameters(
+            parameters,
+            [],
+            {
+                "filter": None,
+                "max_potential": 10000,
+                "exclude_reactions": []
+            },
+        )
+        self.pkgmgr.getpkg("RevBinPkg").build_package(self.parameters["filter"])
+        for metabolite in self.model.metabolites:
+            self.build_potential_variable(metabolite)
+        for reaction in self.model.reactions:
+            if reaction.id[:3] not in ["EX_", "SK_", "DM_"] and reaction.id not in self.parameters["exclude_reactions"]:
+                self.build_dgp_variable(reaction)
+                self.build_dgp_constraint(reaction)
+                self.build_fluxcoupling_constraint(reaction)
+
+    def build_potential_variable(self, object):
+        return self.build_variable(
+            "potential",
+            -1*self.parameters["max_potential"],
+            self.parameters["max_potential"],
+            "continuous",
+            obj,
+        )
+
+    def build_dgp_variable(self, object):
+        return self.build_variable(
+            "dgp",
+            -1*self.parameters["max_potential"],
+            self.parameters["max_potential"],
+            "continuous",
+            object,
+        )
+
+    def build_dgp_constraint(self, object):
+        # Gibbs: dg = Sum(st(i,j)*p(j))
+        # 0 <= (-1) dgp(i) + Sum(st(i,j)*p(j)) <= 0
+        coef = {}
+        for metabolite in object.metabolites:
+            coef[self.variables["potential"][metabolite.id]] = object.metabolites[
+                metabolite
+            ]
+        coef[self.variables["dgp"][object.id]] = -1
+
+        return self.build_constraint(
+            "dgpc", 0, 0, coef, object
+        )
+
+    def build_fluxcoupling_constraint(self, object):
+        # Gibbs: dg = Sum(st(i,j)*p(j)) 
+        #  0 <= dgp(i) + max_energy_magnitude*revbin(i) <= max_energy_magnitude
+        coef = {}
+        coef[self.variables["dgp"][object.id]] = 1
+        coef[self.pkgmgr.getpkg("RevBinPkg").variables["revbin"][object.id]] = self.parameters["max_potential"]+1
+        # build the constraint
+        return self.build_constraint(
+            "thermo", 0, (self.parameters["max_potential"]+1), coef, object
+        )