Support multiple reactions in ratio constraints… (#59)

* feat: add_ratio_constraint supports adding multiple reactions in each side

I changed the add_ratio_constraint method to support adding multiple reactions, linear expressions or lists of reactions to make it possible to create constraints such as:
- v1/(v2 + v3) = r
- (v1 + v2)/v3 = r
- (v1 + v2)/(v3 + v4) = r
- (2 v1 + v2) / v3 = r
- etc...

cameo/core/solver_based_model.py

@@ -401,17 +401,17 @@ def fix_objective_as_constraint(self, time_machine=None, fraction=1):
             time_machine(do=partial(self.solver._add_constraint, constraint, sloppy=True),
                          undo=partial(self.solver.remove, constraint))
 
-    def add_ratio_constraint(self, reaction1, reaction2, ratio, prefix='ratio_constraint_'):
-        """Adds a ratio constraint (reaction1/reaction2 = ratio) to the model.
+    def add_ratio_constraint(self, expr1, expr2, ratio, prefix='ratio_constraint_'):
+        """Adds a ratio constraint (expr1/expr2 = ratio) to the model.
 
         Parameters
         ----------
-        reaction1 : str or Reaction
-            A reaction or a reaction ID.
-        reaction2 : str or Reaction
-            A reaction or a reaction ID.
+        expr1 : str, Reaction, list or sympy.Expression
+            A reaction, a reaction ID or a linear expression.
+        expr2 : str, Reaction, list or sympy.Expression
+            A reaction, a reaction ID or a linear expression.
         ratio : float
-            The ratio in reaction1/reaction2 = ratio
+            The ratio in expr1/expr2 = ratio
         prefix : str
             The prefix that will be added to the constraint ID (defaults to 'ratio_constraint_').
 
@@ -427,13 +427,39 @@ def add_ratio_constraint(self, reaction1, reaction2, ratio, prefix='ratio_constr
         >>> print(model.solver.constraints['ratio_constraint_r1_r2'])
         ratio_constraint: ratio_constraint_r1_r2: 0 <= -0.5 * r1 + 1.0 * PGI <= 0
         """
-        if isinstance(reaction1, six.string_types):
-            reaction1 = self.reactions.get_by_id(reaction1)
-        if isinstance(reaction2, six.string_types):
-            reaction2 = self.reactions.get_by_id(reaction2)
-        ratio_constraint = self.solver.interface.Constraint(
-            reaction1.flux_expression - ratio * reaction2.flux_expression, lb=0, ub=0,
-            name=prefix + reaction1.id + '_' + reaction2.id)
+        if isinstance(expr1, six.string_types):
+            prefix_1 = expr1
+            expr1 = self.reactions.get_by_id(expr1).flux_expression
+        elif isinstance(expr1, Reaction):
+            prefix_1 = expr1.id
+            expr1 = expr1.flux_expression
+        elif isinstance(expr1, list):
+            prefix_1 = "+".join(r.id for r in expr1)
+            expr1 = sum([r.flux_expression for r in expr1], S.Zero)
+        elif not isinstance(expr1, sympy.Expr):
+            raise ValueError("'expr1' is not a valid expression")
+        else:
+            prefix_1 = str(expr1)
+
+        if isinstance(expr2, six.string_types):
+            prefix_2 = expr2
+            expr2 = self.reactions.get_by_id(expr2).flux_expression
+        elif isinstance(expr2, Reaction):
+            prefix_2 = expr2.id
+            expr2 = expr2.flux_expression
+        elif isinstance(expr2, list):
+            prefix_2 = "+".join(r.id for r in expr2)
+            expr2 = sum([r.flux_expression for r in expr2], S.Zero)
+        elif not isinstance(expr2, sympy.Expr):
+            raise ValueError("'expr2' is not a valid expression")
+        else:
+            prefix_2 = str(expr2)
+
+        ratio_constraint = self.solver.interface.Constraint(expr1 - ratio * expr2,
+                                                            lb=0,
+                                                            ub=0,
+                                                            name=prefix + prefix_1 + '_' + prefix_2)
+
         self.solver.add(ratio_constraint, sloppy=True)
         return ratio_constraint
 
@@ -546,7 +572,7 @@ def essential_reactions(self, threshold=1e-6):
         Returns
         -------
         list
-            List of essential reactions.
+            List of essential reactions
         """
         essential = []
         try:

tests/test_solver_based_model.py

@@ -1005,6 +1005,22 @@ def test_add_ratio_constraint(self):
             self.assertAlmostEqual(solution.f, 0.870407873712)
             self.assertAlmostEqual(2 * solution.x_dict['PGI'], solution.x_dict['G6PDH2r'])
 
+            cp = self.model.copy()
+            ratio_constr = cp.add_ratio_constraint('PGI', 'G6PDH2r', 0.5)
+            self.assertEqual(ratio_constr.name, 'ratio_constraint_PGI_G6PDH2r')
+            solution = cp.solve()
+            self.assertAlmostEqual(solution.f, 0.870407873712)
+            self.assertAlmostEqual(2 * solution.x_dict['PGI'], solution.x_dict['G6PDH2r'])
+
+            cp = self.model.copy()
+            ratio_constr = cp.add_ratio_constraint([cp.reactions.PGI, cp.reactions.ACALD],
+                                                   [cp.reactions.G6PDH2r, cp.reactions.ACONTa], 0.5)
+            self.assertEqual(ratio_constr.name, 'ratio_constraint_PGI+ACALD_G6PDH2r+ACONTa')
+            solution = cp.solve()
+            self.assertAlmostEqual(solution.f, 0.8729595694565973)
+            self.assertAlmostEqual(2 * solution.x_dict['PGI'] + solution.x_dict['ACALD'],
+                                   solution.x_dict['G6PDH2r'] + solution.x_dict['ACONTa'])
+
         def test_fix_objective_as_constraint(self):
             # with TimeMachine
             with TimeMachine() as tm: