Sync fbapkg/revbinpkg.py from freiburgermsu fork

modelseedpy/fbapkg/revbinpkg.py

@@ -1,47 +1,47 @@
-# -*- coding: utf-8 -*-
-
-from __future__ import absolute_import
-
-import logging
-from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
-
-# Base class for FBA packages
-class RevBinPkg(BaseFBAPkg):
-    def __init__(self, model):
-        BaseFBAPkg.__init__(
-            self,
-            model,
-            "reversible binary",
-            {"revbin": "reaction"},
-            {"revbinF": "reaction", "revbinR": "reaction"},
-        )
-
-    def build_package(self, filter=None):
-        for reaction in self.model.reactions:
-            # Checking that reaction passes input filter if one is provided
-            if filter == None or reaction.id in filter:
-                self.build_variable(reaction)
-                self.build_constraint(reaction)
-
-    def build_variable(self, object):
-        return BaseFBAPkg.build_variable(self, "revbin", 0, 1, "binary", object)
-
-    def build_constraint(self, object):
-        # -1000 * revbin(i) + forv(i) <= 0
-        BaseFBAPkg.build_constraint(
-            self,
-            "revbinF",
-            None,
-            0,
-            {self.variables["revbin"][object.id]: -1000, object.forward_variable: 1},
-            object,
-        )
-        # 1000 * revbin(i) + revv(i) <= 1000
-        return BaseFBAPkg.build_constraint(
-            self,
-            "revbinR",
-            None,
-            1000,
-            {self.variables["revbin"][object.id]: 1000, object.reverse_variable: 1},
-            object,
-        )
+# -*- coding: utf-8 -*-
+
+from __future__ import absolute_import
+
+import logging
+from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
+
+# Base class for FBA packages
+class RevBinPkg(BaseFBAPkg):
+    def __init__(self, model):
+        BaseFBAPkg.__init__(
+            self,
+            model,
+            "reversible binary",
+            {"revbin": "reaction"},
+            {"revbinF": "reaction", "revbinR": "reaction"},
+        )
+
+    def build_package(self, filter=None):
+        for reaction in self.model.reactions:
+            # Checking that reaction passes input filter if one is provided
+            if filter == None or reaction.id in filter:
+                self.build_variable(reaction)
+                self.build_constraint(reaction)
+
+    def build_variable(self, rxn_obj):
+        return BaseFBAPkg.build_variable(self, "revbin", 0, 1, "binary", rxn_obj)
+
+    def build_constraint(self, rxn_obj):
+        # -1000 * revbin(i) + forv(i) <= 0
+        BaseFBAPkg.build_constraint(
+            self,
+            "revbinF",
+            None,
+            0,
+            {self.variables["revbin"][rxn_obj.id]: -1000, rxn_obj.forward_variable: 1},
+            rxn_obj,
+        )
+        # 1000 * revbin(i) + revv(i) <= 1000
+        return BaseFBAPkg.build_constraint(
+            self,
+            "revbinR",
+            None,
+            1000,
+            {self.variables["revbin"][rxn_obj.id]: 1000, rxn_obj.reverse_variable: 1},
+            rxn_obj,
+        )