Index
A
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
U
|
V
|
W
A
add_modcell_fields() (in module src.support.cobra_modeling)
add_to_design_table() (in module src.@MCdesign)
addMetabolite_updated() (in module src.support.cobra_modeling.cobra_toolbox_updates)
addReaction_updated() (in module src.support.cobra_modeling.cobra_toolbox_updates)
C
calc_enum_penalty_obj_fun() (in module src.@MCdesign)
calc_flux_table() (in module src.@ResAnalysis)
calc_penalty_obj_fun() (in module src.@MCdesign)
calc_prod_envelope() (in module src.@ResAnalysis)
calc_prod_envelope_s() (in module src.@ResAnalysis)
change_unknown_bounds() (in module src.support.cobra_modeling)
check_mets_in_rxn() (ProductionNetworkDebugger method)
check_parent_fields() (in module src.support.cobra_modeling)
checkMassChargeBalance_fixed() (in module src.support.cobra_modeling.cobra_toolbox_updates)
combine_module_variables() (in module src.@MCdesign)
compatibility() (in module src.@ResAnalysis)
consistent_solutions (ResAnalysis attribute)
cont_jaccard() (in module src.support.modcell2)
convert_external_solution_to_modcell() (in module src.support.cobra_modeling)
create_consistent_solutions() (in module src.@ResAnalysis)
create_initial_population() (in module src.@MCdesign)
create_knowledge_based_initial_population() (in module src.@MCdesign)
create_problem_directory() (in module src.support.modcell2)
crossover_module_variable() (in module src.@MCdesign)
D
deep_copy() (in module src.support.general)
default_bounds_from_rxn_str() (in module src.support.cobra_modeling)
default_figure_info (ResAnalysis attribute)
default_plot_lines (ResAnalysis attribute)
design_parameters (MCdesign attribute)
design_table (MCdesign attribute)
distinguishable_colors() (in module src.support.general)
drop_empty_elements() (in module src.support.general)
E
enum_parameters (MCdesign attribute)
enumerate_alternative_solutions() (in module src.@MCdesign)
enumerate_alternative_solutions_one_target() (in module src.@MCdesign)
escher_input_from_pFBA_table() (in module src.@ResAnalysis)
exclusive_gene_map() (in module src.support.cobra_modeling)
extract_alternative_solutions() (in module src.@MCdesign)
extract_module_variables() (in module src.@MCdesign)
F
fcm_get_table() (in module src.@ResAnalysis)
fcm_scan_c() (in module src.@ResAnalysis)
find_dominated_rows() (in module src.@MCdesign)
findBlockedReaction_fast() (in module src.support.cobra_modeling)
findFullCoSets() (in module src.support.cobra_modeling.candidate_determination)
findHiCarbonRxns_updated() (in module src.support.cobra_modeling.cobra_toolbox_updates)
findTransRxns_updated() (in module src.support.cobra_modeling.cobra_toolbox_updates)
flux_tol (ProductionNetworkDebugger attribute)
G
ga_parameters (MCdesign attribute)
get_CPF() (in module src.@ResAnalysis)
get_mapped_gpr() (in module src.support.cobra_modeling)
get_met_ids_from_rxn_str() (in module src.support.cobra_modeling)
graph_deletion_frequency() (in module src.@ResAnalysis)
graph_sequential_implementation() (in module src.@ResAnalysis)
graph_sequential_implementation_s() (in module src.@ResAnalysis)
growth_to_nongrowth_designs() (in module src.@MCdesign)
H
het_rxn_id (ProductionNetworkDebugger attribute)
I
identify_deletion_role() (in module src.@ResAnalysis)
inspect() (ProductionNetworkDebugger method)
is_wt_points_calc (ResAnalysis attribute)
L
let_loc() (in module src.support.general)
load_prodnet() (in module src.support.modcell2)
load_solutions() (in module src.@ResAnalysis)
lookup_design_table() (in module src.@MCdesign)
M
map_non_cand_rxn_to_gene() (in module src.support.cobra_modeling)
max_design_table_size (MCdesign attribute)
MCdesign (class in src.@MCdesign)
MCdesign() (MCdesign method)
mutationuniform_module() (in module src.@MCdesign)
N
N_OBJ_DIGITS (MCdesign attribute)
n_solutions (ResAnalysis attribute)
number_cores (MCdesign attribute)
O
OBJ_TOL (MCdesign attribute)
optimize_cofactor_turnover() (in module src.support.cobra_modeling)
P
padcat() (in module src.support.general)
parseMetNames_updated() (in module src.support.cobra_modeling.cobra_toolbox_updates)
piechart_deletion_frequency() (in module src.@ResAnalysis)
piechart_deletion_frequency_w() (in module src.@ResAnalysis)
plot_2d_pf() (in module src.@ResAnalysis)
plot_compatibility() (in module src.@ResAnalysis)
plot_design_tradeoff() (in module src.@ResAnalysis)
plot_fva_range() (in module src.@ResAnalysis)
plot_pareto_front() (in module src.@ResAnalysis)
plot_pca() (in module src.@ResAnalysis)
plot_yield_vs_growth() (in module src.@ResAnalysis)
plot_yield_vs_growth_s() (in module src.@ResAnalysis)
pn (ProductionNetworkDebugger attribute)
print_design() (in module src.@ResAnalysis)
printSeparator() (in module src.support.general)
prodnet (MCdesign attribute)
(ResAnalysis attribute)
production_envelope() (in module src.support.cobra_modeling.cobra_toolbox_updates)
ProductionNetworkDebugger (class in src.support.cobra_modeling)
R
random_number_seed (MCdesign attribute)
read_dict() (in module src.support.general)
read_sheet() (in module src.support.general)
reformat_cgo() (in module src.support.general)
remove_always_zero_prod() (in module src.@ResAnalysis)
remove_products() (in module src.@ResAnalysis)
ResAnalysis (class in src.@ResAnalysis)
ResAnalysis() (ResAnalysis method)
S
save_mop_solution() (in module src.@MCdesign)
save_no_overwrite() (in module src.support.general)
save_pdf() (in module src.support.general)
set_default_ga_parameters() (in module src.@MCdesign)
set_design_parameters() (in module src.@MCdesign)
set_figure_defaults() (in module src.support.general)
set_solution_state() (in module src.@ResAnalysis)
set_start_point() (in module src.@MCdesign)
similarity_plots() (in module src.@ResAnalysis)
singleGeneDeletion_parallel() (in module src.support.cobra_modeling.cobra_toolbox_updates)
singleRxnDeletion_parallel() (in module src.support.cobra_modeling.cobra_toolbox_updates)
solution_ids (ResAnalysis attribute)
solutions (ResAnalysis attribute)
solve_lp() (in module src.support.modcell2)
solve_mop() (in module src.@MCdesign)
solve_mop_for_stall_gen() (in module src.@MCdesign)
src.@MCdesign (module)
src.@ResAnalysis (module)
src.support.cobra_modeling (module)
src.support.cobra_modeling.candidate_determination (module)
src.support.cobra_modeling.cobra_toolbox_updates (module)
src.support.general (module)
src.support.modcell2 (module)
start_parallel() (in module src.support.general)
start_point (MCdesign attribute)
stepwise_implementation() (in module src.@ResAnalysis)
U
use_module_variable (MCdesign attribute)
V
vector_difference_tolerance (MCdesign attribute)
W
write_csv() (in module src.support.general)
write_result_tables() (in module src.@ResAnalysis)
write_to_xls() (in module src.@ResAnalysis)
wt_all_growth_rates (ResAnalysis attribute)
wt_all_product_yields (ResAnalysis attribute)
ModCell2
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