bugfixes

src/PAModelpy/Enzyme.py

@@ -13,7 +13,7 @@
 from optlang.symbolics import Zero
 
 from .CatalyticEvent import CatalyticEvent
-from typing import Dict, Union, Optional
+from typing import Dict, Union, Optional, Literal
 from warnings import warn
 
 def _change_catalytic_event_list_to_dictlist_after_unpickling(self):
@@ -97,7 +97,7 @@ def kcat_values(self):
 
     @property
     def concentration(
-        self, units: str = "mmol/gDW", return_units: bool = False
+        self, units: Literal['mmol/gDW', 'g/gDW'] = "mmol/gDW", return_units: bool = False
     ) -> float:
         """Returns the enzyme's total concentration considering any associated reactions.
 
@@ -113,11 +113,11 @@ def concentration(
         concentration = self.enzyme_variable.concentration
         if units == 'g/gDW':
             #converting mmol to grams of protein:
-            # [g] = [mmol]* 1e-3 [mol/mmol] * MW[g/mol] *1e-6 [solver tolerance conversion factor]
-            concentration = concentration * 1e-3 * self.molmass*1e-6
+            # [g] = [mmol]* 1e-3 [mol/mmol] * MW[g/mol]
+            concentration = concentration * 1e-3 * self.molmass
         if return_units:
-            return concentration*1e-6, units
-        return concentration*1e-6
+            return concentration, units
+        return concentration
 
     @concentration.setter
     def concentration(self, conc):

src/PAModelpy/EnzymeSectors.py

@@ -160,7 +160,6 @@ def add(self, model):
                         if rxn_id in rxn2protein.keys():
                             del rxn2protein[rxn_id]
                 except:
-                    print(model.reactions.query(rxn_id))
                     warn(
                         f"Reaction {rxn_id} is not in the model, this reaction will be skipped"
                     )
@@ -194,6 +193,11 @@ def add(self, model):
                 if enzyme_id in model.enzyme_variables and not self._enzyme_is_enzyme_complex(protein_reaction, enzyme_id):
                     enzyme = model.enzymes.get_by_id(enzyme_id)
                     self._add_reaction_to_enzyme(model, enzyme, rxn_id, kcat)
+                    self.rxn2protein[rxn_id] = {**self.rxn2protein[rxn_id],
+                                                **{enzyme_id: {
+                                                    **kcat,
+                                                    'genes': enzyme.genes,
+                                                    'protein_reaction_association': protein_reaction}}}
 
                 else:
                     if self.protein2gene != {}:
@@ -208,7 +212,6 @@ def add(self, model):
                         molmass=molmass,
                         genes=gene_list
                     )
-
                     if self._enzyme_is_enzyme_complex(protein_reaction, enzyme_id):
                         for pr in protein_reaction:
                             if len(pr) > 1:
@@ -252,7 +255,6 @@ def add(self, model):
 
                     # adding to the enzyme sector object for easy removal
                     model.tpc += 1
-
         return model
 
     def check_kcat_values(self, model, reaction, enzyme_dict):

src/PAModelpy/PAModel.py

@@ -264,8 +264,8 @@ def parameter_filter(enz: Enzyme) -> bool:
 
                 # check kcat values
                 for kcatdict in kcats.values():
-                    for kcat in kcatdict.values():
-                        if kcat < 0:
+                    for kcat_dict in kcatdict.values():
+                        if kcat_dict < 0:
                             # invalid kcat value
                             warnings.warn(
                                 'Turnover number for reaction "'
@@ -276,7 +276,8 @@ def parameter_filter(enz: Enzyme) -> bool:
 
                 # extract reaction from model
                 reaction = self.reactions.get_by_id(rxn_id)
-                for kcats in kcats.values():
+
+                for kcat_dict in kcats.values():
                     # check consistency between provided kcat values and reaction direction
                     if self._sensitivity:
                         lower_bound = -self.constraints[f"{rxn_id}_lb"].ub
@@ -286,23 +287,23 @@ def parameter_filter(enz: Enzyme) -> bool:
                         upper_bound = reaction.upper_bound
                     if lower_bound >= 0 and upper_bound > 0:
                         # reaction is irreversible in the forward direction
-                        if "f" not in kcats:  # or 'b' in kcats:
+                        if "f" not in kcat_dict:  # or 'b' in kcats:
                             warnings.warn(
                                 rxn_id
                                 + ": Inconsistencies between the reaction reversibility and the provided kcat values"
                             )
                             return False
                     elif lower_bound < 0 and upper_bound <= 0:
                         # reaction is irreversible in the backward direction
-                        if "b" not in kcats or "f" in kcats:
+                        if "b" not in kcats or "f" in kcat_dict:
                             warnings.warn(
                                 rxn_id
                                 + ": Inconsistencies between the reaction reversibility and the provided kcat values"
                             )
                             return False
                     else:
                         # reaction is reversible
-                        if "f" not in kcats:  # or 'b' not in kcats:
+                        if "f" not in kcat_dict:  # or 'b' not in kcats:
                             warnings.warn(
                                 rxn_id
                                 + ": Inconsistencies between the reaction reversibility and the provided kcat values"
@@ -1338,12 +1339,14 @@ def change_reaction_bounds(
     def change_reaction_ub(self, rxn_id: str, upper_bound: float = None):
         if self._sensitivity:
             self.constraints[rxn_id + "_ub"].ub = upper_bound
+            self.reactions.get_by_id(rxn_id).upper_bound = upper_bound*0.01
         else:
             self.reactions.get_by_id(rxn_id).upper_bound = upper_bound
 
     def change_reaction_lb(self, rxn_id: str, lower_bound: float = None):
         if self._sensitivity:
             self.constraints[rxn_id + "_lb"].ub = -lower_bound
+            self.reactions.get_by_id(rxn_id).lower_bound = lower_bound*0.01
         else:
             self.reactions.get_by_id(rxn_id).lower_bound = lower_bound