Index

A | B | C | D | E | F | G | I | L | M | N | O | P | Q | R | S | T | U | W

A

add_gene_reaction_rule() (cobra.core.Reaction.Reaction method)
add_legacy_test() (in module cobra.test.solvers)
add_metabolites() (cobra.core.ArrayBasedModel.ArrayBasedModel method)
(cobra.core.Model.Model method)
(cobra.core.Reaction.Reaction method)
add_new_test() (in module cobra.test.solvers)
add_reaction() (cobra.core.Model.Model method)
add_reactions() (cobra.core.ArrayBasedModel.ArrayBasedModel method)
(cobra.core.Model.Model method)
add_sbml_species() (in module cobra.io.sbml)
add_test() (in module cobra.test.solvers)
append() (cobra.core.DictList.DictList method)
ArrayBasedModel (class in cobra.core.ArrayBasedModel)
assess_medium_component_essentiality() (in module cobra.flux_analysis.essentiality)
assess_objective() (in module cobra.flux_analysis.objective)

B

build_reaction_string() (cobra.core.Reaction.Reaction method)

C

calculate_formula_weight() (cobra.core.Formula.Formula method)
check_mass_balance() (cobra.core.Reaction.Reaction method)
cobra.__init__ (module)
cobra.core (module)
cobra.core.ArrayBasedModel (module)
cobra.core.DictList (module)
cobra.core.Formula (module)
cobra.core.Gene (module)
cobra.core.Metabolite (module)
cobra.core.Model (module)
cobra.core.Object (module)
cobra.core.Reaction (module)
cobra.core.Solution (module)
cobra.external.ppmap (module)
cobra.flux_analysis (module)
cobra.flux_analysis.double_deletion (module)
cobra.flux_analysis.essentiality (module)
cobra.flux_analysis.moma (module)
cobra.flux_analysis.objective (module)
cobra.flux_analysis.single_deletion (module)
cobra.flux_analysis.variability (module)
cobra.io (module)
cobra.io.mat (module)
cobra.io.sbml (module)
cobra.manipulation (module)
cobra.manipulation.delete (module)
cobra.manipulation.modify (module)
cobra.mlab (module)
cobra.mlab.mlab (module)
cobra.solvers (module)
cobra.solvers.glpk_solver (module)
cobra.solvers.legacy (module)
cobra.solvers.parameters (module)
cobra.stats (module)
cobra.stats.stats (module)
cobra.test (module)
cobra.test.flux_analysis (module)
cobra.test.parallel (module)
cobra.test.solvers (module)
cobra.test.unit_tests (module)
cobra.topology (module)
cobra.topology.reporter_metabolites (module)
cobra_model_object_to_cobra_matlab_struct() (in module cobra.mlab.mlab)
CobraTestCase (class in cobra.test.unit_tests)
combine_p_values() (in module cobra.stats.stats)
convert_rule_to_boolean_rule() (in module cobra.manipulation.modify)
convert_to_irreversible() (in module cobra.manipulation.modify)
copy() (cobra.core.ArrayBasedModel.ArrayBasedModel method)
(cobra.core.Metabolite.Metabolite method)
(cobra.core.Model.Model method)
(cobra.core.Reaction.Reaction method)
create_cobra_model_from_sbml_file() (in module cobra.io.sbml)
create_problem() (in module cobra.solvers.glpk_solver)
create_test_model() (in module cobra.test)
create_test_suite() (in module cobra.test)

D

delete() (cobra.core.Reaction.Reaction method)
delete_model_genes() (in module cobra.manipulation.delete)
deletion_analysis() (in module cobra.flux_analysis.essentiality)
DictList (class in cobra.core.DictList)
double_deletion() (in module cobra.flux_analysis.double_deletion)
double_gene_deletion() (in module cobra.flux_analysis.double_deletion)

E

endswith() (cobra.core.Object.Object method)
error_weighted() (in module cobra.stats.stats)
extend() (cobra.core.DictList.DictList method)

F

find_blocked_reactions() (in module cobra.flux_analysis.variability)
fix_legacy_id() (in module cobra.io.sbml)
flux_variability_analysis() (in module cobra.flux_analysis.variability)
flux_variability_analysis_wrapper() (in module cobra.flux_analysis.variability)
format_solution() (in module cobra.solvers.glpk_solver)
Formula (class in cobra.core.Formula)

G

Gene (class in cobra.core.Gene)
get_by_id() (cobra.core.DictList.DictList method)
get_coefficient() (cobra.core.Reaction.Reaction method)
get_coefficients() (cobra.core.Reaction.Reaction method)
get_compartments() (cobra.core.Reaction.Reaction method)
get_gene() (cobra.core.Reaction.Reaction method)
get_id() (in module cobra.core.DictList)
get_model() (cobra.core.Metabolite.Metabolite method)
(cobra.core.Reaction.Reaction method)
get_products() (cobra.core.Reaction.Reaction method)
get_reactants() (cobra.core.Reaction.Reaction method)
get_reaction() (cobra.core.Metabolite.Metabolite method)
get_status() (in module cobra.solvers.glpk_solver)
guided_copy() (cobra.core.Gene.Gene method)
(cobra.core.Metabolite.Metabolite method)
(cobra.core.Object.Object method)
(cobra.core.Reaction.Reaction method)

I

identify_reporter_metabolites() (in module cobra.topology.reporter_metabolites)
index() (cobra.core.DictList.DictList method)
init_matlab_toolbox() (in module cobra.mlab.mlab)
initialize_growth_medium() (in module cobra.manipulation.modify)
insert() (cobra.core.DictList.DictList method)

L

list_attr() (cobra.core.DictList.DictList method)
load_matlab_model() (in module cobra.io.mat)

M

matlab_cell_to_python_list() (in module cobra.mlab.mlab)
matlab_cobra_struct_to_python_cobra_object() (in module cobra.mlab.mlab)
matlab_logical_to_python_logical() (in module cobra.mlab.mlab)
matlab_sparse_to_numpy_array() (in module cobra.mlab.mlab)
matlab_sparse_to_scipy_sparse() (in module cobra.mlab.mlab)
Metabolite (class in cobra.core.Metabolite)
Model (class in cobra.core.Model)
moma() (in module cobra.flux_analysis.moma)

N

numpy_array_to_mlab_sparse() (in module cobra.mlab.mlab)

O

Object (class in cobra.core.Object)
optimize() (cobra.core.Model.Model method)
(in module cobra.solvers)

P

p_adjust() (in module cobra.stats.stats)
parse_composition() (cobra.core.Formula.Formula method)
(cobra.core.Metabolite.Metabolite method)
parse_gene_association() (cobra.core.Reaction.Reaction method)
parse_legacy_id() (in module cobra.io.sbml)
parse_legacy_sbml_notes() (in module cobra.io.sbml)
pop() (cobra.core.DictList.DictList method)
(cobra.core.Reaction.Reaction method)
ppmap() (in module cobra.external.ppmap)
ppmap_identify_reporter_metabolites() (in module cobra.topology.reporter_metabolites)
print_values() (cobra.core.Reaction.Reaction method)
process_prefixed_reaction() (cobra.core.Reaction.Reaction method)
prune_unused_metabolites() (in module cobra.manipulation.delete)
prune_unused_reactions() (in module cobra.manipulation.delete)
python_list_to_matlab_cell() (in module cobra.mlab.mlab)

Q

query() (cobra.core.DictList.DictList method)

R

Reaction (class in cobra.core.Reaction)
read_legacy_sbml() (in module cobra.io.sbml)
reconstruct_reaction() (cobra.core.Reaction.Reaction method)
remove() (cobra.core.DictList.DictList method)
remove_from_model() (cobra.core.Gene.Gene method)
(cobra.core.Metabolite.Metabolite method)
(cobra.core.Reaction.Reaction method)
remove_reactions() (cobra.core.Model.Model method)
reverse() (cobra.core.DictList.DictList method)
revert_to_reversible() (in module cobra.manipulation.modify)
run_fva() (in module cobra.flux_analysis.variability)

S

save_matlab_model() (cobra.test.unit_tests.TestCobraIO method)
(in module cobra.io.mat)
scipy_sparse_to_mlab_sparse() (in module cobra.mlab.mlab)
set_parameter() (in module cobra.solvers.glpk_solver)
setUp() (cobra.test.flux_analysis.TestCobraFluxAnalysis method)
(cobra.test.solvers.TestCobraSolver method)
(cobra.test.unit_tests.CobraTestCase method)
(cobra.test.unit_tests.TestDictList method)
single_deletion() (in module cobra.flux_analysis.single_deletion)
single_gene_deletion() (in module cobra.flux_analysis.single_deletion)
single_reaction_deletion() (in module cobra.flux_analysis.single_deletion)
Solution (class in cobra.core.Solution)
solve() (in module cobra.solvers.glpk_solver)
solve_problem() (in module cobra.solvers.glpk_solver)
sort() (cobra.core.DictList.DictList method)
startswith() (cobra.core.Object.Object method)
subtract_metabolites() (cobra.core.Reaction.Reaction method)

T

test_add_reaction() (cobra.test.unit_tests.TestCobraCore method)
test_all() (in module cobra.test)
(in module cobra.test.flux_analysis)
(in module cobra.test.solvers)
(in module cobra.test.unit_tests)
test_copy() (cobra.test.unit_tests.TestCobraCore method)
test_double_deletion() (cobra.test.flux_analysis.TestCobraFluxAnalysis method)
test_flux_variability() (cobra.test.flux_analysis.TestCobraFluxAnalysis method)
test_glpk_attributes() (cobra.test.solvers.TestCobraSolver method)
test_glpk_create() (cobra.test.solvers.TestCobraSolver method)
test_glpk_feasible_solve() (cobra.test.solvers.TestCobraSolver method)
test_glpk_independent_creation() (cobra.test.solvers.TestCobraSolver method)
test_glpk_infeasible_solve() (cobra.test.solvers.TestCobraSolver method)
test_glpk_solve_minimize() (cobra.test.solvers.TestCobraSolver method)
test_glpk_solve_mip() (cobra.test.solvers.TestCobraSolver method)
test_mat_read_write() (cobra.test.unit_tests.TestCobraIO method)
test_single_deletion() (cobra.test.flux_analysis.TestCobraFluxAnalysis method)
test_solvers() (in module cobra.solvers.legacy)
testAdd() (cobra.test.unit_tests.TestDictList method)
testAppend() (cobra.test.unit_tests.TestDictList method)
TestCobraCore (class in cobra.test.unit_tests)
TestCobraFluxAnalysis (class in cobra.test.flux_analysis)
TestCobraIO (class in cobra.test.unit_tests)
TestCobraSolver (class in cobra.test.solvers)
TestDictList (class in cobra.test.unit_tests)
testExtend() (cobra.test.unit_tests.TestDictList method)
testIadd() (cobra.test.unit_tests.TestDictList method)
to_array_based_model() (cobra.core.Model.Model method)

U

undelete_model_genes() (in module cobra.manipulation.delete)
union() (cobra.core.DictList.DictList method)
update() (cobra.core.ArrayBasedModel.ArrayBasedModel method)
(cobra.core.Model.Model method)
update_objective() (in module cobra.flux_analysis.objective)
update_problem() (in module cobra.solvers.glpk_solver)

W

write_cobra_model_to_sbml_file() (in module cobra.io.sbml)