added functionality to remove the active enzyme sector + unit tests

src/PAModelpy/Enzyme.py

@@ -2,7 +2,6 @@
  - Enzyme: Constraints relating enzymes to reactions. Including upper and lower bound enzyme constraints
  - EnzymeVariable: Variable related to an enzyme. The value of this variable represent the concentration.
 """
-import PAModelpy.Enzyme
 import cobra.core
 import cobra
 from cobra import Reaction, Object

src/PAModelpy/PAModel.py

@@ -1290,23 +1290,24 @@ def remove_catalytic_events(self,
                     self.remove_cons_vars(enzyme._constraints)
 
     def remove_sectors(self,
-                       sectors: Union[str, Sector, ActiveEnzymeSector, List[Union[str, Sector, ActiveEnzymeSector]]]
+                       sectors: Union[str, Sector, ActiveEnzymeSector]
                        )-> None:
         """Remove sections from the model.
 
             Also removes associated CatalyticEvents if they exist.
 
-                Parameters
-                ----------
-                secotrs : list or sector or str
+            Args:
+                sectors : list or sector or str
                     A list with sector (`PAModelpy.Sector` or `PAModelpy.ActiveEnzymeSector`), or their id's, to remove.
                     A single sector will be placed in a list. Str will be placed in a list and used to
-                    find the secotr in the model.
+                    find the sector in the model.
                 """
         if isinstance(sectors, str) or hasattr(sectors, "id"):
             sectors = [sectors]
 
         for sector in sectors:
+            if isinstance(sector, str): sector = self.sectors.get_by_id(sector)
+
             print(f'Removing the following protein sector: {sector.id}\n')
             # remove the connection to the model
             sector._model = None
@@ -1317,50 +1318,101 @@ def remove_sectors(self,
             except ValueError:
                 warnings.warn(f"{sector.id} not in {self}")
 
-            # remove the sector from the total protein if it is there
-            if self.TOTAL_PROTEIN_CONSTRAINT_ID in self.constraints.keys():
-                # remove parts of constraint corresponding to the enzyme sector from the total_protein_constraint
-                # 1. add the intercept value from the sum of protein (Total_protein == Etot)
-                tpc_ub = self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID].ub
-                self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID].ub = tpc_ub + sector.intercept
-
-                # 2. remove link between flux and enzyme concentration
-                # link enzyme concentration in the sector to the total enzyme concentration
-                lin_rxn = self.reactions.get_by_id(sector.id_list[0])
-                self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID].set_linear_coefficients({
-                    lin_rxn.forward_variable: 0,
-                    lin_rxn.reverse_variable: 0
-                })
-
+            #check if the sector is the ActiveEnzymeSector, this needs to have a different removal mechanism
+            if isinstance(sector, ActiveEnzymeSector):
+                self.remove_active_enzymes_sector(sector)
             else:
+                self.remove_linear_sector(sector)
+
+    def remove_active_enzymes_sector(self, sector: ActiveEnzymeSector) -> None:
+        """
+            Remove an active enzyme sector from the model.
+
+            This function performs the following steps:
+            1. Removes all enzymes associated with the sector.
+            2. Removes all catalytic events associated with the sector.
+            3. If a total protein constraint exists, it removes this constraint.
+            4. Deletes the sector constraint from the model's easy lookup.
+            5. Removes the sector from the model and disconnects its link to the model.
+
+            Args:
+                sector (ActiveEnzymeSector): The active enzyme sector to be removed.
+
+            Returns:
+                None
+            """
+
+        self.remove_enzymes(self.enzymes.copy())
+        self.remove_catalytic_events(self.catalytic_events)
+        if self.TOTAL_PROTEIN_CONSTRAINT_ID in self.constraints.keys():
+            # remove total_protein_constraint
+            self.remove_cons_vars(self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID])
+
+        # remove the sector and its connection to the model
+        self.sectors.remove(sector)
+        sector._model = None
+
+    def remove_linear_sector(self, sector: Union[UnusedEnzymeSector, TransEnzymeSector, CustomSector]) -> None:
+        """
+            Remove a linear sector from the model.
+
+            This function performs the following steps:
+            1. If a total protein constraint exists, it adjusts the constraint to remove the sector's contribution.
+            2. Removes the associated constraints and variables.
+            3. Deletes the sector constraint from the model's easy lookup.
+            4. Removes the sector from the model and disconnects its link to the model.
+
+            Args:
+                sector (Union[UnusedEnzymeSector, TransEnzymeSector, CustomSector]): The linear sector to be removed.
+
+            Returns:
+                None
+            """
+        # remove the sector from the total protein if it is there
+        if self.TOTAL_PROTEIN_CONSTRAINT_ID in self.constraints.keys():
+            # remove parts of constraint corresponding to the enzyme sector from the total_protein_constraint
+            # 1. add the intercept value from the sum of protein (Total_protein == Etot)
+            tpc_ub = self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID].ub
+            self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID].ub = tpc_ub + sector.intercept
+
+            # 2. remove link between flux and enzyme concentration
+            # link enzyme concentration in the sector to the total enzyme concentration
+            lin_rxn = self.reactions.get_by_id(sector.id_list[0])
+            self.constraints[self.TOTAL_PROTEIN_CONSTRAINT_ID].set_linear_coefficients({
+                lin_rxn.forward_variable: 0,
+                lin_rxn.reverse_variable: 0
+            })
+
+        else:
+
+            # remove the associated constraints
+            for constraint in sector.constraints:
+                if isinstance(constraint, Enzyme):
+                    self.remove_enzymes([constraint])
+                # check if constraint is in the solver
+                if constraint in self.constraints.values():
+                    self.remove_cons_vars([constraint])
+                    self.solver.update()
+
+            # remove the associated variables
+            for variable in sector.variables:
+                if isinstance(variable, CatalyticEvent):
+                    self.remove_catalytic_events([variable])
+                else:
+                    self.remove_cons_vars([variable])
+                    self.solver.update()
+                    # remove reference to the sector variables in all groups
+                    associated_groups = self.get_associated_groups(variable)
+                    for group in associated_groups:
+                        group.remove_members(variable)
+
+            # remove sector constraint from model easy lookup:
+            del self.sector_constraints[sector.id]
+
+        # remove the sector and its connection to the model
+        self.sectors.remove(sector)
+        sector._model = None
 
-                #remove the associated constraints
-                for constraint in sector.constraints:
-                    if isinstance(constraint, Enzyme):
-                        self.remove_enzymes([constraint])
-                    #check if constraint is in the solver
-                    if constraint in self.constraints.values():
-                        self.remove_cons_vars([constraint])
-                        self.solver.update()
-
-                #remove the associated variables
-                for variable in sector.variables:
-                    if isinstance(variable, CatalyticEvent):
-                        self.remove_catalytic_events([variable])
-                    else:
-                        self.remove_cons_vars([variable])
-                        self.solver.update()
-                        # remove reference to the sector variables in all groups
-                        associated_groups = self.get_associated_groups(variable)
-                        for group in associated_groups:
-                            group.remove_members(variable)
-
-                # remove sector constraint from model easy lookup:
-                del self.sector_constraints[sector.id]
-
-            #remove the sector and its connection to the model
-            self.sectors.remove(sector)
-            sector._model = None
 
     def test(self, glc_flux: Union[int, float]=10):
         """

src/PAModelpy/__init__.py

@@ -1 +1,7 @@
-print('Loading PAModelpy modules version 0.0.3.4')
+print('Loading PAModelpy modules version 0.0.3.11')
+
+from .Enzyme import *
+from .EnzymeSectors import *
+from .CatalyticEvent import *
+from .PAModel import *
+from .configuration import *

tests/unit_tests/test_pamodel.py → tests/unit_tests/test_pamodel/test_pamodel.py

@@ -8,11 +8,7 @@
             os.path.dirname( #testing dir
                 os.path.dirname(__file__))))) #this dir
 
-from src.PAModelpy.PAModel import PAModel
-from src.PAModelpy.configuration import Config
-from src.PAModelpy.EnzymeSectors import ActiveEnzymeSector, UnusedEnzymeSector, TransEnzymeSector
-
-
+from src.PAModelpy import PAModel,Config,ActiveEnzymeSector, UnusedEnzymeSector, TransEnzymeSector
 
 def test_if_pamodel_change_kcat_function_works():
     #arrange
@@ -132,6 +128,39 @@ def test_if_pamodel_enzyme_get_kcat_values_correctly():
     # assert
     assert kcat_to_return == kcat_returned['f']
 
+def test_if_pamodel_remove_sectors_can_remove_active_enzyme_sector():
+    # Arrange
+    toy_pam = build_toy_pam(sensitivity=False)
+
+    # Act
+    toy_pam.remove_sectors('ActiveEnzymeSector')
+
+    # Assert
+    assert len(toy_pam.enzymes) == 0
+    assert all('EC_' not in key for key in toy_pam.constraints.keys())
+    assert toy_pam.TOTAL_PROTEIN_CONSTRAINT_ID not in toy_pam.constraints.keys()
+
+def test_if_pamodel_remove_sectors_can_remove_translational_protein_sector():
+    # Arrange
+    toy_pam = build_toy_pam(sensitivity=False)
+    sector = toy_pam.sectors.get_by_id('TranslationalProteinSector')
+    lin_rxn = toy_pam.reactions.get_by_id(sector.id_list[0])
+
+    # get the old upperbound for the total protein constraint
+    tpc_ub = toy_pam.constraints[toy_pam.TOTAL_PROTEIN_CONSTRAINT_ID].ub
+
+    # Act
+    toy_pam.remove_sectors('TranslationalProteinSector')
+
+    #make sure the linear coefficients associated to the sector in the total protein constriant are 0
+    lin_coeff = toy_pam.constraints[toy_pam.TOTAL_PROTEIN_CONSTRAINT_ID].get_linear_coefficients([
+        lin_rxn.forward_variable,
+        lin_rxn.reverse_variable,
+    ])
+
+    # Assert
+    assert toy_pam.constraints[toy_pam.TOTAL_PROTEIN_CONSTRAINT_ID].ub == tpc_ub + sector.intercept
+    assert all(coeff == 0 for coeff in lin_coeff.values())
 
 #######################################################################################################
 #HELPER METHODS