Index

A

analyze_div_enum_results() (in module dexom_python.enum_functions.enumeration)

apply_gpr() (in module dexom_python.gpr_rules)

C

calc_objval_from_flux() (in module dexom_python.result_functions) check_constraint_values() (in module dexom_python.model_functions) check_model_options() (in module dexom_python.model_functions) check_model_primals() (in module dexom_python.model_functions) check_reaction_weights() (in module dexom_python.enum_functions.enumeration) check_threshold_tolerance() (in module dexom_python.model_functions) combine_binary_solutions_and_fluxes() (in module dexom_python.enum_functions.enumeration) compile_solutions() (in module dexom_python.result_functions)

create_enum_variables() (in module dexom_python.enum_functions.enumeration) create_full_variable_single() (in module dexom_python.imat_functions) create_full_variables() (in module dexom_python.imat_functions) create_icut_constraint() (in module dexom_python.enum_functions.icut_functions) create_maxdist_objective() (in module dexom_python.enum_functions.maxdist_functions) create_new_partial_variable_single() (in module dexom_python.imat_functions) create_new_partial_variables() (in module dexom_python.imat_functions) create_optimality_constraint() (in module dexom_python.imat_functions) create_reaction() (in module dexom_python.toy_models)

D

dagNet() (in module dexom_python.toy_models) dexom_python module dexom_python.cluster_utils module dexom_python.cluster_utils.solution_compilation module dexom_python.enum_functions module dexom_python.enum_functions.diversity_enum_functions module dexom_python.enum_functions.enumeration module dexom_python.enum_functions.icut_functions module dexom_python.enum_functions.maxdist_functions module dexom_python.enum_functions.permutation_functions module

dexom_python.enum_functions.riptide_functions module dexom_python.enum_functions.rxn_enum_functions module dexom_python.gpr_rules module dexom_python.imat_functions module dexom_python.model_functions module dexom_python.pathway_enrichment module dexom_python.result_functions module dexom_python.toy_models module diversity_enum() (in module dexom_python.enum_functions.diversity_enum_functions)

E

EnumSolution (class in dexom_python.enum_functions.enumeration)

expression2qualitative() (in module dexom_python.gpr_rules)

F

Fisher_groups() (in module dexom_python.pathway_enrichment)

Fisher_subsystems() (in module dexom_python.pathway_enrichment)

G

get_all_reactions_from_model() (in module dexom_python.model_functions)

get_recent_solution_and_iteration() (in module dexom_python.enum_functions.enumeration) get_subsystems_from_model() (in module dexom_python.model_functions)

I

icut() (in module dexom_python.enum_functions.icut_functions) imat() (in module dexom_python.imat_functions)

imat_riptide_like() (in module dexom_python.enum_functions.riptide_functions) ImatException

L

load_reaction_weights() (in module dexom_python.model_functions)

M

maxdist() (in module dexom_python.enum_functions.maxdist_functions) module dexom_python dexom_python.cluster_utils dexom_python.cluster_utils.solution_compilation dexom_python.enum_functions dexom_python.enum_functions.diversity_enum_functions dexom_python.enum_functions.enumeration dexom_python.enum_functions.icut_functions dexom_python.enum_functions.maxdist_functions dexom_python.enum_functions.permutation_functions dexom_python.enum_functions.riptide_functions dexom_python.enum_functions.rxn_enum_functions dexom_python.gpr_rules dexom_python.imat_functions dexom_python.model_functions dexom_python.pathway_enrichment dexom_python.result_functions dexom_python.toy_models

P

parsimonious_imat() (in module dexom_python.imat_functions) perform_ora() (in module dexom_python.pathway_enrichment)

permute_genelabels() (in module dexom_python.enum_functions.permutation_functions) plot_Fisher_pathways() (in module dexom_python.pathway_enrichment) plot_pca() (in module dexom_python.result_functions)

R

r13m10() (in module dexom_python.toy_models) read_model() (in module dexom_python.model_functions) read_prev_sol() (in module dexom_python.enum_functions.enumeration)

read_solution() (in module dexom_python.result_functions) replace_MulMax_AddMin() (in module dexom_python.gpr_rules) rxn_enum() (in module dexom_python.enum_functions.rxn_enum_functions) RxnEnumSolution (class in dexom_python.enum_functions.rxn_enum_functions)

S

save_reaction_weights() (in module dexom_python.model_functions)

small4M() (in module dexom_python.toy_models) small4S() (in module dexom_python.toy_models)

W

write_solution() (in module dexom_python.result_functions)