Critical fix in add_reactions.

Adding a new reaction would nullify an existing objective.
biosustain · May 7, 2015 · a5f259d · a5f259d
1 parent e2c77e5
commit a5f259d
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/cameo/core/solver_based_model.py b/cameo/core/solver_based_model.py
@@ -216,7 +216,7 @@ def _populate_solver(self, reaction_list):
                 constr_terms[metabolite.id].append(sympy.Mul._from_args([sympy.RealNumber(-1*coeff), reverse_variable]))
 
             if reaction.objective_coefficient != 0.:
-                objective_terms.append(sympy.Mul._from_args((sympy.RealNumber(reaction.objective_coefficient), reaction.flux_expression)))
+                objective_terms.append(reaction.objective_coefficient * reaction.flux_expression)
 
         for met_id, terms in six.iteritems(constr_terms):
             expr = sympy.Add._from_args(terms)
@@ -225,8 +225,11 @@ def _populate_solver(self, reaction_list):
             except KeyError:
                 self.solver._add_constraint(self.solver.interface.Constraint(expr, name=met_id, lb=0, ub=0), sloppy=True)
 
-        objective_expression = sympy.Add._from_args(objective_terms)
-        self.solver.objective = self.solver.interface.Objective(objective_expression, name='obj', direction='max')
+        objective_expression = sympy.Add(*objective_terms)
+        if self.solver.objective is None:
+            self.solver.objective = self.solver.interface.Objective(objective_expression, name='obj', direction='max')
+        else:
+            self.solver.objective += objective_expression
 
     def add_reactions(self, reaction_list):
         cloned_reaction_list = list()

diff --git a/tests/test_solver_based_model.py b/tests/test_solver_based_model.py
@@ -506,10 +506,15 @@ def test_add_reactions(self):
         r2 = Reaction('r2')
         r2.add_metabolites({Metabolite('A'): -1, Metabolite('C'): 1, Metabolite('D'): 1})
         r2.lower_bound, r2.upper_bound = 0., 999999.
+        r2.objective_coefficient = 3.
         self.model.add_reactions([r1, r2])
         self.assertEqual(self.model.reactions[-2], r1)
         self.assertEqual(self.model.reactions[-1], r2)
         self.assertTrue(isinstance(self.model.reactions[-2].reverse_variable, self.model.solver.interface.Variable))
+        self.assertEqual(self.model.objective.expression.coeff(self.model.reactions.Biomass_Ecoli_core_N_LPAREN_w_FSLASH_GAM_RPAREN__Nmet2.forward_variable), 1.)
+        self.assertEqual(self.model.objective.expression.coeff(self.model.reactions.Biomass_Ecoli_core_N_LPAREN_w_FSLASH_GAM_RPAREN__Nmet2.reverse_variable), -1.)
+        self.assertEqual(self.model.objective.expression.coeff(self.model.reactions.r2.forward_variable), 3.)
+        self.assertEqual(self.model.objective.expression.coeff(self.model.reactions.r2.reverse_variable), -3.)
 
     def test_all_objects_point_to_all_other_correct_objects(self):
         model = load_model(os.path.join(TESTDIR, 'data/EcoliCore.xml'))