From ebe380ccfdcf82a0dce099bac336f3064dfabc70 Mon Sep 17 00:00:00 2001
From: "samira.vandenbogaard" <samira.vandenbogaard@gmail.com>
Date: Tue, 30 Jul 2024 17:19:12 +0200
Subject: [PATCH] bugfixes related to pamparametrizer

---
 Scripts/pam_generation_uniprot_id.py |  8 +++++++-
 src/PAModelpy/Enzyme.py              | 24 ++++++++++++++++++++++++
 src/PAModelpy/EnzymeSectors.py       |  5 ++++-
 src/PAModelpy/PAModel.py             | 12 ++++++------
 4 files changed, 41 insertions(+), 8 deletions(-)

diff --git a/Scripts/pam_generation_uniprot_id.py b/Scripts/pam_generation_uniprot_id.py
index 7074a25..b68f603 100644
--- a/Scripts/pam_generation_uniprot_id.py
+++ b/Scripts/pam_generation_uniprot_id.py
@@ -276,7 +276,7 @@ def parse_reaction2protein(enzyme_db: pd.DataFrame, model:cobra.Model) -> dict:
             # no enzyme information found
             print('No enzyme information found for reaction: ' + rxn.id)
             enzyme_id = 'Enzyme_' + rxn.id
-            gpr_info = parse_gpr_information_for_protein2genes(rxn.gpr, rxn_id)
+            gpr_info = parse_gpr_information_for_protein2genes(rxn.gpr)
 
             rxn2protein[rxn.id] = {enzyme_id: {
                 **kcat_dict,
@@ -439,3 +439,9 @@ def filter_sublists(nested_list, target_string):
     ecoli_pam.change_reaction_bounds('EX_glc__D_e', -10, 0)
     ecoli_pam.optimize()
     print(ecoli_pam.objective.value)
+    import pickle
+
+    with open('path_to_your_pickle_file.pkl', 'wb') as file:
+        p = pickle.dump(ecoli_pam, file)
+    with open('path_to_your_pickle_file.pkl', 'rb') as file:
+        ob = pickle.load(file)
diff --git a/src/PAModelpy/Enzyme.py b/src/PAModelpy/Enzyme.py
index 62ae1e3..a4cdf0b 100644
--- a/src/PAModelpy/Enzyme.py
+++ b/src/PAModelpy/Enzyme.py
@@ -380,6 +380,30 @@ def add_enzymes(self, enzymes: DictList):
                     else:
                         self._model.enzymes.append(enzyme)
 
+    def __copy__(self) -> "EnzymeComplex":
+        """Copy the enzyme complex.
+
+        Returns:
+            PAModelpy.Enzyme.EnzymeComplex: A new enzyme complex that is a copy of the original enzyme.
+        """
+
+        cop = copy(super(EnzymeComplex, self))
+        return cop
+
+    def __deepcopy__(self, memo: dict) -> "EnzymeComplex":
+        """Copy the enzyme complex with memo.
+
+        Args:
+            memo (dict): Automatically passed parameter.
+
+        Returns:
+            PAModelpy.Enzyme.EnzymeComplex: A new enzyme complex that is a copy of the original enzyme with memo.
+        """
+
+        cop = deepcopy(super(EnzymeComplex, self), memo)
+        return cop
+
+
 class EnzymeVariable(Reaction):
     """EnzymeVariable is a class for holding information regarding the variable representing an enzyme in the model.
     For each reaction, the enzyme variables are summarized in a CatalyticEvent.
diff --git a/src/PAModelpy/EnzymeSectors.py b/src/PAModelpy/EnzymeSectors.py
index bb8db70..712ec48 100644
--- a/src/PAModelpy/EnzymeSectors.py
+++ b/src/PAModelpy/EnzymeSectors.py
@@ -176,7 +176,10 @@ def add(self, model):
                 kcat = dict(
                     (k, v) for k, v in enzyme_dict.items() if k == "f" or k == "b"
                 )
-                protein_reaction = enzyme_dict['protein_reaction_association']
+                if 'protein_reaction_association' in enzyme_dict.keys():
+                    protein_reaction = enzyme_dict['protein_reaction_association']
+                else:
+                    protein_reaction = enzyme_id
 
                 # get molar mass of enzyme or replace with default value
                 if "molmass" in enzyme_dict.keys():
diff --git a/src/PAModelpy/PAModel.py b/src/PAModelpy/PAModel.py
index 1f5ee13..d7674fb 100644
--- a/src/PAModelpy/PAModel.py
+++ b/src/PAModelpy/PAModel.py
@@ -999,7 +999,6 @@ def calculate_csc(self, obj_value, mu, mu_ub, mu_lb, mu_ec_f, mu_ec_b):
                 len(self.capacity_sensitivity_coefficients)
             ] = new_row_LB
 
-        print(self.enzymes)
         for enzyme in self.enzymes:
             for catalyzing_enzyme in self._get_catalyzing_enzymes_for_enzyme(enzyme):
                 ce = self.enzymes.get_by_id(catalyzing_enzyme)
@@ -1168,12 +1167,13 @@ def change_total_protein_constraint(self, p_tot):
         self.solver.update()
 
     def change_sector_parameters(
-        self, sector, slope: float, intercept: float, lin_rxn_id: str
+        self, sector, slope: float, intercept: float, lin_rxn_id: str, print_change = False
     ):
-        # input in g/gDW
-        print(f"Changing the slope and intercept of the {sector.id}")
-        print(f"Changing slope from {sector.slope} to {slope*1e3} mg/gcdw/h")
-        print(f"Changing intercept from {sector.intercept} to {intercept*1e3} mg/gcdw")
+        if print_change:
+            # input in g/gDW
+            print(f"Changing the slope and intercept of the {sector.id}")
+            print(f"Changing slope from {sector.slope} to {slope*1e3} mg/gcdw/h")
+            print(f"Changing intercept from {sector.intercept} to {intercept*1e3} mg/gcdw")
 
         prev_intercept = sector.intercept
         # *1e3 to convert g to mg