Fixing a couple of minor bugs and added new variable class (#35)

Thank you @remidhum 

* FIX: fixed the apply_directionality function

solution.raw dataframe index does not contain the fwd and bwd use variables.

* ENH: added new binary variable class

This class is usefull to deal with inactive reactions in a model.

* ENH: deal with models without an objective function

Objective function is set to Zero (symbol("0") does not work!) if there is no defined objective function

* OOPS: change proper function ...

* FIX: fixed the failing test

As suggested, I added a check to determine what object type is passed.

* MNT: solution object type testing improved

pytfa/analysis/manipulation.py

@@ -1,3 +1,6 @@
+from ..core.model import Solution
+import pandas as pd
+
 def apply_reaction_variability(tmodel, va, inplace = True):
     """
     Applies the VA results as bounds for the reactions of a cobra_model
@@ -46,7 +49,7 @@ def apply_generic_variability(tmodel,va, inplace = True):
     return _tmodel
 
 
-def apply_directionality(tmodel,solution, inplace = True):
+def apply_directionality(tmodel, solution, inplace = True):
     """
     Takes a flux solution and transfers its reaction directionality as
     constraints for the cobra_model
@@ -62,15 +65,22 @@ def apply_directionality(tmodel,solution, inplace = True):
     else:
         _tmodel = tmodel.copy()
 
+    if isinstance(solution, Solution):
+        sol = solution.raw
+    elif isinstance(solution, pd.Series) or isinstance(solution, pd.DataFrame):
+        sol = solution
+    else:
+        raise ArgumentError('solution object should be of class Solution or pandas.Series')
+
     for this_reaction in _tmodel.reactions:
 
         backward_use = _tmodel.backward_use_variable.get_by_id(this_reaction.id)
         forward_use = _tmodel.forward_use_variable.get_by_id(this_reaction.id)
 
-        backward_use.variable.lb = round(solution.raw[backward_use.name])
-        backward_use.variable.ub = round(solution.raw[backward_use.name])
+        backward_use.variable.lb = round(sol[backward_use.name])
+        backward_use.variable.ub = round(sol[backward_use.name])
 
-        forward_use.variable.lb  = round(solution.raw[forward_use.name])
-        forward_use.variable.ub  = round(solution.raw[forward_use.name])
+        forward_use.variable.lb  = round(sol[forward_use.name])
+        forward_use.variable.ub  = round(sol[forward_use.name])
 
-    return _tmodel
+    return _tmodel

pytfa/io/dict.py

@@ -22,6 +22,8 @@
 
 from copy import copy
 
+import sympy
+
 
 def get_all_subclasses(cls):
     all_subclasses = []
@@ -371,8 +373,11 @@ def model_from_dict(obj, solver=None, custom_hooks = None):
     return new
 
 def rebuild_obj_from_dict(new, objective_dict):
-    obj_expr = symbol_sum([v*new.variables.get(x) for x,v in objective_dict.items()])
-    new.objective = obj_expr
+    if objective_dict.__class__ is dict:
+        obj_expr = symbol_sum([v*new.variables.get(x) for x,v in objective_dict.items()])
+        new.objective = obj_expr
+    else:
+        new.objective = sympy.S.Zero
 
 def add_custom_classes(model, custom_hooks):
     """
@@ -446,5 +451,3 @@ def _rebuild_stoichiometry(new, stoich):
     return defaultdict(int,
                        {new.metabolites.get_by_id(k):v
                         for k,v in stoich.items()})
-
-

pytfa/optim/variables.py

@@ -454,7 +454,6 @@ def model(self):
 
     prefix = 'MV_'
 
-
 class ForwardUseVariable(ReactionVariable, BinaryVariable):
     """
     Class to represent a forward use variable, a type of binary variable used to
@@ -486,6 +485,24 @@ def __init__(self, reaction, **kwargs):
 
     prefix = 'BU_'
 
+class ForwardBackwardUseVariable(ReactionVariable, BinaryVariable):
+    """
+    Class to represent a type of binary variable used to tell whether the
+    reaction is active or not such that:
+        FU + BU + BFUSE = 1
+    """
+
+    def __init__(self, reaction, **kwargs):
+        if not 'lb' in kwargs:
+            kwargs['lb'] = 0
+        if not 'ub' in kwargs:
+            kwargs['ub'] = 1
+
+        ReactionVariable.__init__(self, reaction,
+                                  type=get_binary_type(),
+                                  **kwargs)
+
+    prefix = 'BFUSE_'
 
 class LogConcentration(MetaboliteVariable):
     """
@@ -494,23 +511,20 @@ class LogConcentration(MetaboliteVariable):
 
     prefix = 'LC_'
 
-
 class DeltaGErr(ReactionVariable):
     """
     Class to represent a DeltaGErr
     """
 
     prefix = 'DGE_'
 
-
 class DeltaG(ReactionVariable):
     """
     Class to represent a DeltaG
     """
 
     prefix = 'DG_'
 
-
 class DeltaGstd(ReactionVariable):
     """
     Class to represent a DeltaG^o (naught) - standard conditions
@@ -536,7 +550,6 @@ def __init__(self,reaction,**kwargs):
 
     prefix = 'PosSlack_'
 
-
 class NegSlackVariable(ReactionVariable):
     """
     Class to represent a negative slack variable for relaxation problems
@@ -554,4 +567,3 @@ class PosSlackLC(MetaboliteVariable):
 class NegSlackLC(MetaboliteVariable):
 
     prefix = 'NegSlackLC_'
-