Merge remote-tracking branch 'origin/mcPAModelpy' into mcPAModelpy

# Conflicts: # docs/PAM_setup_guide.md # tests/unit_tests/test_pamodel/test_pam_setup.py # tests/unit_tests/test_pamodel/test_pamodel.py
iAMB-RWTH-Aachen · Jan 28, 2025 · 68b3772 · 68b3772
2 parents 912560b + b3334a9
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diff --git a/Data/Surface_growth_rate_data/MSA_Supplementary_DataS3.xlsx b/Data/Surface_growth_rate_data/MSA_Supplementary_DataS3.xlsx
diff --git a/Data/Surface_growth_rate_data/MSA_Supplementary_DataS4.xlsx b/Data/Surface_growth_rate_data/MSA_Supplementary_DataS4.xlsx
diff --git a/Data/Surface_growth_rate_data/surface_mumax.xlsx b/Data/Surface_growth_rate_data/surface_mumax.xlsx
diff --git a/Data/eGFP_expression_Bienick2014.xls b/Data/eGFP_expression_Bienick2014.xls
diff --git a/Data/eGFP_protein_sequence.txt b/Data/eGFP_protein_sequence.txt
diff --git a/Data/enzyme_sets.json b/Data/enzyme_sets.json
diff --git a/Data/mcPAM_iML1515_EnzymaticData.xlsx b/Data/mcPAM_iML1515_EnzymaticData.xlsx
diff --git a/Data/proteinAllocationModel_iML1515_EnzymaticData_py.xls b/Data/proteinAllocationModel_iML1515_EnzymaticData_py.xls
diff --git a/Data/proteinAllocationModel_iML1515_EnzymaticData_py_uniprot.xlsx b/Data/proteinAllocationModel_iML1515_EnzymaticData_py_uniprot.xlsx
diff --git a/Data/proteinAllocationModel_mc-core_EnzymaticData_241209_multi.xlsx b/Data/proteinAllocationModel_mc-core_EnzymaticData_241209_multi.xlsx
diff --git a/Data/proteinAllocationModel_mciML1515_EnzymaticData_241209_multi.xlsx b/Data/proteinAllocationModel_mciML1515_EnzymaticData_241209_multi.xlsx
diff --git a/Data/proteome_data_extract_schmidt2016.xlsx b/Data/proteome_data_extract_schmidt2016.xlsx
diff --git a/Examples/mcpam_generator.py b/Examples/mcpam_generator.py
@@ -1,24 +1,44 @@
 from Scripts.mcpam_simulations_analysis import (run_pam_mcpam_core_with_optimized_kcats,
-                                                 run_simulations_pam_mcpam,
+                                                 run_simulation_pam_mcpam,
+                                                 run_simulations_pam_mcpam_w_different_areas,
                                                  set_up_ecolicore_pam,
                                                  set_up_ecolicore_mcpam,
+                                                 set_up_ecolicore_mcpam_new_surface_parameter,
                                                  compare_mu_for_different_sensitivities_ecolicore_pam,
                                                  perform_single_gene_ko_for_all_genes,
                                                  perform_and_plot_single_KO)
 from Scripts.mcpam_generation_uniprot_id import set_up_ecoli_mcpam, set_up_ecoli_pam
+from Scripts.mcpam_toy_generation import build_toy_model
+from src.PAModelpy.utils.pam_generation import set_up_pam, set_up_core_pam
 import matplotlib.pyplot as plt; plt.rcdefaults()
 
 if __name__ == "__main__":
+    # Build full scale pam new parsing
+    pam_info_path = 'Data/proteinAllocationModel_mciML1515_EnzymaticData_241209_multi.xlsx'
+    pam = set_up_pam(pam_info_file=pam_info_path, sensitivity=False, membrane_sector=False)
+    mcpam = set_up_pam(pam_info_file=pam_info_path, sensitivity=False, membrane_sector=True)
 
-    pam = set_up_ecoli_pam(sensitivity=False)
-    mcpam = set_up_ecoli_mcpam(sensitivity=False)
-
-    # pam, mcpam = run_pam_mcpam_core_with_optimized_kcats(sensitivity=True, type='full scale', enzyme_sets_name="enzyme_sets.json")
     models = [pam, mcpam]
-    run_simulations_pam_mcpam(models, type="full scale")
+    run_simulation_pam_mcpam(models, type="full scale")
+
+    # Build core pam
+    # pam = set_up_ecolicore_pam(sensitivity=False)
+    # mcpam = set_up_ecolicore_mcpam_new_surface_parameter(sensitivity=False)
+    # models = [pam, mcpam]
+    # run_simulations_pam_mcpam_w_different_areas(models, type='core')
+
+    # Build core pam new parse
+    # pam = set_up_core_pam(sensitivity=False, membrane_sector=False, pam_info_file='Data/proteinAllocationModel_mc-core_EnzymaticData_241209_multi.xlsx')
+    # mcpam = set_up_core_pam(sensitivity=False, membrane_sector=True, pam_info_file='Data/proteinAllocationModel_mc-core_EnzymaticData_241209_multi.xlsx')
+    # models = [pam, mcpam]
+    # run_simulation_pam_mcpam(models, type="core")
+
+    # Build toy pam
+    # toy_pam = build_toy_model(membrane_sector=True)
+    # toy_pam.objective = "R11"
+    # toy_pam.optimize()
+    # print(toy_pam.objective.value)
 
-    for protein, kcats in mcpam.sectors.get_by_id("MembraneSector").membrane_proteins.items():
-        print(protein, kcats)
 
 
 

diff --git a/Examples/toy_model_generator.py b/Examples/toy_model_generator.py