Documentation for dexom_python

• DEXOM in python
  • Requirements
    • Installing CPLEX
  • Functions
    • apply_gpr
    • iMAT
    • enum_functions
  • Parallelized DEXOM
  • Examples
    • Toy models
    • Recon 2.2
    • Cell-specific reconstruction
• dexom_python package top-level modules
  • Submodules
  • model_functions module
    • check_model_options()
    • check_threshold_tolerance()
    • get_all_reactions_from_model()
    • get_subsystems_from_model()
    • load_reaction_weights()
    • read_model()
    • save_reaction_weights()
  • gpr_rules module
    • apply_gpr()
    • expression2qualitative()
    • main()
    • replace_MulMax_AddMin()
  • imat_functions module
    • ImatException
    • create_full_variable_single()
    • create_full_variables()
    • create_new_partial_variable_single()
    • create_new_partial_variables()
    • imat()
    • main()
  • result_functions module
    • compile_solutions()
    • main()
    • plot_pca()
    • read_solution()
    • write_solution()
  • toy_models module
    • create_reaction()
    • dagNet()
    • r13m10()
    • small4M()
    • small4S()
  • pathway_enrichment module
    • Fisher_groups()
    • Fisher_subsystems()
    • main()
    • plot_Fisher_pathways()
  • Module contents
• dexom_python.enum_functions enumeration modules
  • Submodules
  • enumeration module
    • EnumSolution
    • analyze_div_enum_results()
    • combine_binary_solutions()
    • create_enum_variables()
    • get_recent_solution_and_iteration()
    • read_prev_sol()
  • rxn_enum_functions module
    • RxnEnumSolution
    • main()
    • rxn_enum()
  • icut_functions module
    • create_icut_constraint()
    • icut()
    • main()
  • maxdist_functions module
    • create_maxdist_constraint()
    • create_maxdist_objective()
    • main()
    • maxdist()
  • diversity_enum_functions module
    • diversity_enum()
    • main()
  • Module contents
• dexom_python.cluster_utils modules
  • Submodules
  • write_cluster_scripts module
    • main()
    • write_batch_script1()
    • write_batch_script2()
    • write_batch_script_divenum()
    • write_rxn_enum_script()
  • dexom_cluster_results module
    • analyze_dexom_cluster_results()
    • main()
  • solution_compilation module
    • main()
  • Module contents
• CHANGELOG
  • Versions 0.x
    • 0.5:
    • 0.4:
    • 0.3:
    • 0.2:

Indices and tables

• Index

• Module Index

• Search Page