cobra
0.13.3
1. Getting Started
2. Building a Model
3. Reading and Writing Models
4. Simulating with FBA
5. Simulating Deletions
6. Production envelopes
7. Flux sampling
8. Loopless FBA
9. Gapfillling
10. Growth media
11. Solvers
12. Tailored constraints, variables and objectives
13. Using the COBRA toolbox with cobrapy
14. FAQ
15. Sphinx AutoAPI Index
cobra
Docs
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
_
__add__() (cobra.core.dictlist.DictList method)
(cobra.core.formula.Formula method)
(cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
__build_problem() (cobra.flux_analysis.sampling.HRSampler method)
__call__() (cobra.util.context.HistoryManager method)
(documentation_builder.conf.Mock method)
__contains__() (cobra.core.dictlist.DictList method)
__copy__() (cobra.core.dictlist.DictList method)
(cobra.core.reaction.Reaction method)
__deepcopy__() (cobra.core.reaction.Reaction method)
__delitem__() (cobra.core.dictlist.DictList method)
__delslice__() (cobra.core.dictlist.DictList method)
__dir__() (cobra.core.dictlist.DictList method)
(cobra.core.solution.Solution method)
__enter__() (cobra.core.model.Model method)
__exit__() (cobra.core.model.Model method)
__getattr__() (cobra.core.dictlist.DictList method)
(documentation_builder.conf.Mock method)
__getitem__() (cobra.core.dictlist.DictList method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.util.util.AutoVivification method)
__getslice__() (cobra.core.dictlist.DictList method)
__getstate__() (cobra.core.dictlist.DictList method)
(cobra.core.model.Model method)
(cobra.core.object.Object method)
(cobra.core.species.Species method)
(cobra.flux_analysis.sampling.OptGPSampler method)
__iadd__() (cobra.core.dictlist.DictList method)
(cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
__imul__() (cobra.core.reaction.Reaction method)
__init__() (cobra.core.dictlist.DictList method)
(cobra.core.formula.Formula method)
(cobra.core.gene.GPRCleaner method)
(cobra.core.gene.Gene method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.model.Model method)
(cobra.core.object.Object method)
(cobra.core.reaction.Reaction method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.core.species.Species method)
(cobra.exceptions.OptimizationError method)
(cobra.flux_analysis.gapfilling.GapFiller method)
(cobra.flux_analysis.sampling.ACHRSampler method)
(cobra.flux_analysis.sampling.HRSampler method)
(cobra.flux_analysis.sampling.OptGPSampler method)
(cobra.manipulation.delete._GeneRemover method)
(cobra.util.context.HistoryManager method)
(documentation_builder.conf.Mock method)
__isub__() (cobra.core.dictlist.DictList method)
(cobra.core.reaction.Reaction method)
__mul__() (cobra.core.reaction.Reaction method)
__reduce__() (cobra.core.dictlist.DictList method)
__repr__() (cobra.core.object.Object method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
__setitem__() (cobra.core.dictlist.DictList method)
__setslice__() (cobra.core.dictlist.DictList method)
__setstate__() (cobra.core.dictlist.DictList method)
(cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
__single_iteration() (cobra.flux_analysis.sampling.ACHRSampler method)
__str__() (cobra.core.object.Object method)
(cobra.core.reaction.Reaction method)
__sub__() (cobra.core.dictlist.DictList method)
(cobra.core.reaction.Reaction method)
_add_cycle_free() (in module cobra.flux_analysis.loopless)
_as_medium() (in module cobra.medium.minimal_medium)
_associate_gene() (cobra.core.reaction.Reaction method)
_bounds_dist() (cobra.flux_analysis.sampling.HRSampler method)
_cell() (in module cobra.io.mat)
_check() (cobra.core.dictlist.DictList method)
(in module cobra.io.mat)
_dissociate_gene() (cobra.core.reaction.Reaction method)
_element_lists() (in module cobra.flux_analysis.deletion)
_entities_ids() (in module cobra.flux_analysis.deletion)
_escape_str_id() (in module cobra.manipulation.modify)
_extend_nocheck() (cobra.core.dictlist.DictList method)
_fix_type() (in module cobra.io.dict)
_gene_deletion() (in module cobra.flux_analysis.deletion)
_gene_deletion_worker() (in module cobra.flux_analysis.deletion)
_GeneEscaper (class in cobra.manipulation.modify)
_generate_index() (cobra.core.dictlist.DictList method)
_GeneRemover (class in cobra.manipulation.delete)
_get_growth() (in module cobra.flux_analysis.deletion)
_get_id_compartment() (in module cobra.io.mat)
_init_worker() (in module cobra.flux_analysis.deletion)
_is_redundant() (cobra.flux_analysis.sampling.HRSampler method)
_multi_deletion() (in module cobra.flux_analysis.deletion)
_optimize_or_value() (in module cobra.flux_analysis.reaction)
_populate_solver() (cobra.core.model.Model method)
_process_flux_dataframe() (in module cobra.flux_analysis.summary)
_random_point() (cobra.flux_analysis.sampling.HRSampler method)
_reaction_deletion() (in module cobra.flux_analysis.deletion)
_reaction_deletion_worker() (in module cobra.flux_analysis.deletion)
_reactions_knockouts_with_restore() (in module cobra.flux_analysis.deletion)
_replace_on_id() (cobra.core.dictlist.DictList method)
_repr_html_() (cobra.core.gene.Gene method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
(cobra.core.solution.Solution method)
_reproject() (cobra.flux_analysis.sampling.HRSampler method)
_sample_chain() (in module cobra.flux_analysis.sampling)
_set_id_with_model() (cobra.core.metabolite.Metabolite method)
(cobra.core.object.Object method)
(cobra.core.reaction.Reaction method)
_step() (in module cobra.flux_analysis.sampling)
_update_awareness() (cobra.core.reaction.Reaction method)
_update_optional() (in module cobra.io.dict)
_valid_atoms() (in module cobra.util.solver)
_warn_format() (in module cobra)
A
ACHRSampler (class in cobra.flux_analysis.sampling)
add() (cobra.core.dictlist.DictList method)
add_absolute_expression() (in module cobra.util.solver)
add_boundary() (cobra.core.model.Model method)
add_cons_vars() (cobra.core.model.Model method)
add_cons_vars_to_problem() (in module cobra.util.solver)
add_envelope() (in module cobra.flux_analysis.phenotype_phase_plane)
add_linear_obj() (in module cobra.medium.minimal_medium)
add_loopless() (in module cobra.flux_analysis.loopless)
add_metabolites() (cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
add_mip_obj() (in module cobra.medium.minimal_medium)
add_moma() (in module cobra.flux_analysis.moma)
add_pfba() (in module cobra.flux_analysis.parsimonious)
add_reaction() (cobra.core.model.Model method)
add_reactions() (cobra.core.model.Model method)
add_room() (in module cobra.flux_analysis.room)
add_sbml_species() (in module cobra.io.sbml)
add_SBO() (in module cobra.manipulation.annotate)
add_switches_and_objective() (cobra.flux_analysis.gapfilling.GapFiller method)
annotate_cobra_from_sbml() (in module cobra.io.sbml3)
annotate_sbml_from_cobra() (in module cobra.io.sbml3)
append() (cobra.core.dictlist.DictList method)
assert_optimal() (in module cobra.util.solver)
assess() (in module cobra.flux_analysis.reaction)
assess_component() (in module cobra.flux_analysis.reaction)
assess_precursors() (in module cobra.flux_analysis.reaction)
assess_products() (in module cobra.flux_analysis.reaction)
ast2str() (in module cobra.core.gene)
attribute() (in module cobra.test.test_io_order)
AutoVivification (class in cobra.util.util)
B
Basic (class in cobra.io.sbml3)
batch() (cobra.flux_analysis.sampling.HRSampler method)
benchmark_to_df() (in module scripts.compare-benchmark)
boundary() (cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
bounds() (cobra.core.reaction.Reaction method)
,
[1]
build_hugo_md() (in module scripts.publish_release)
build_reaction_from_string() (cobra.core.reaction.Reaction method)
build_reaction_string() (cobra.core.reaction.Reaction method)
C
captured_output() (in module cobra.test.test_flux_analysis)
center (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
check_in_line() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
check_line() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
check_mass_balance() (cobra.core.reaction.Reaction method)
(in module cobra.manipulation.validate)
check_metabolite_compartment_formula() (in module cobra.manipulation.validate)
check_reaction_bounds() (in module cobra.manipulation.validate)
check_solver_status() (in module cobra.util.solver)
choose_solver() (in module cobra.util.solver)
clip() (in module cobra.io.sbml3)
cobra (module)
cobra.core (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.core.species (module)
cobra.exceptions (module)
cobra.flux_analysis (module)
cobra.flux_analysis.deletion (module)
cobra.flux_analysis.gapfilling (module)
cobra.flux_analysis.geometric (module)
cobra.flux_analysis.loopless (module)
cobra.flux_analysis.moma (module)
cobra.flux_analysis.parsimonious (module)
cobra.flux_analysis.phenotype_phase_plane (module)
cobra.flux_analysis.reaction (module)
cobra.flux_analysis.room (module)
cobra.flux_analysis.sampling (module)
cobra.flux_analysis.summary (module)
cobra.flux_analysis.variability (module)
cobra.io (module)
cobra.io.dict (module)
cobra.io.json (module)
cobra.io.mat (module)
cobra.io.sbml (module)
cobra.io.sbml3 (module)
cobra.io.yaml (module)
cobra.manipulation (module)
cobra.manipulation.annotate (module)
cobra.manipulation.delete (module)
cobra.manipulation.modify (module)
cobra.manipulation.validate (module)
cobra.medium (module)
cobra.medium.boundary_types (module)
cobra.medium.minimal_medium (module)
cobra.test (module)
cobra.test.conftest (module)
cobra.test.test_flux_analysis (module)
cobra.test.test_io (module)
cobra.test.test_io_order (module)
cobra.test.test_manipulation (module)
cobra.test.test_medium (module)
cobra.test.test_model (module)
cobra.test.test_solver_model (module)
cobra.test.test_solver_utils (module)
cobra.test.test_util (module)
cobra.util (module)
cobra.util.array (module)
cobra.util.context (module)
cobra.util.solver (module)
cobra.util.util (module)
CobraSBMLError (class in cobra.io.sbml3)
compare_matrices() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
compare_models() (cobra.test.test_io.TestCobraIO method)
compartments() (cobra.core.model.Model method)
,
[1]
(cobra.core.reaction.Reaction method)
constraint() (cobra.core.metabolite.Metabolite method)
constraint_matrices() (in module cobra.util.array)
constraints() (cobra.core.model.Model method)
construct_geometric_fba_model() (in module cobra.test.test_flux_analysis)
construct_gpr_xml() (in module cobra.io.sbml3)
construct_ll_test_model() (in module cobra.test.test_flux_analysis)
construct_loopless_model() (in module cobra.flux_analysis.loopless)
construct_room_model() (in module cobra.test.test_flux_analysis)
construct_room_solution() (in module cobra.test.test_flux_analysis)
convert_to_irreversible() (in module cobra.manipulation.modify)
copy() (cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
(cobra.core.species.Species method)
create_cobra_model_from_sbml_file() (in module cobra.io.sbml)
create_mat_dict() (in module cobra.io.mat)
create_mat_metabolite_id() (in module cobra.io.mat)
create_stoichiometric_matrix() (in module cobra.util.array)
create_test_model() (in module cobra.test)
D
data_directory() (in module cobra.test.conftest)
delete() (cobra.core.reaction.Reaction method)
delete_model_genes() (in module cobra.manipulation.delete)
demands() (cobra.core.model.Model method)
description() (cobra.core.model.Model method)
,
[1]
dict_list() (in module cobra.test.test_util)
DictList (class in cobra.core.dictlist)
documentation_builder.conf (module)
documentation_builder.plot_helper (module)
double_gene_deletion() (in module cobra.flux_analysis.deletion)
double_reaction_deletion() (in module cobra.flux_analysis.deletion)
dress_results() (cobra.core.solution.LegacySolution method)
E
elements() (cobra.core.metabolite.Metabolite method)
,
[1]
empty_model() (in module cobra.test.conftest)
empty_once() (in module cobra.test.conftest)
escape_ID() (in module cobra.manipulation.modify)
eval_gpr() (in module cobra.core.gene)
exchanges() (cobra.core.model.Model method)
extend() (cobra.core.dictlist.DictList method)
extend_model() (cobra.flux_analysis.gapfilling.GapFiller method)
extra_comparisons() (cobra.test.test_io.TestCobraIO method)
extract_rdf_annotation() (in module cobra.io.sbml3)
F
f (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
f() (cobra.core.solution.Solution method)
FeasibleButNotOptimal (class in cobra.exceptions)
fill() (cobra.flux_analysis.gapfilling.GapFiller method)
find_blocked_reactions() (in module cobra.flux_analysis.variability)
find_boundary_types() (in module cobra.medium.boundary_types)
find_bump() (in module scripts.publish_release)
find_carbon_sources() (in module cobra.flux_analysis.phenotype_phase_plane)
find_essential_genes() (in module cobra.flux_analysis.variability)
find_essential_reactions() (in module cobra.flux_analysis.variability)
find_external_compartment() (in module cobra.medium.boundary_types)
find_gene_knockout_reactions() (in module cobra.manipulation.delete)
fix_legacy_id() (in module cobra.io.sbml)
fix_objective_as_constraint() (in module cobra.util.solver)
flux() (cobra.core.reaction.Reaction method)
flux_expression() (cobra.core.reaction.Reaction method)
flux_variability_analysis() (in module cobra.flux_analysis.variability)
fluxes (cobra.core.solution.Solution attribute)
format_long_string() (in module cobra.util.util)
Formula (class in cobra.core.formula)
formula_weight() (cobra.core.metabolite.Metabolite method)
forward_variable() (cobra.core.reaction.Reaction method)
from_json() (in module cobra.io.json)
from_mat_struct() (in module cobra.io.mat)
from_yaml() (in module cobra.io.yaml)
functional() (cobra.core.gene.Gene method)
,
[1]
(cobra.core.reaction.Reaction method)
fva_results() (in module cobra.test.conftest)
fwd_idx (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
G
gapfill() (in module cobra.flux_analysis.gapfilling)
GapFiller (class in cobra.flux_analysis.gapfilling)
Gene (class in cobra.core.gene)
gene_from_dict() (in module cobra.io.dict)
gene_name_reaction_rule() (cobra.core.reaction.Reaction method)
gene_reaction_rule() (cobra.core.reaction.Reaction method)
,
[1]
gene_to_dict() (in module cobra.io.dict)
generate_fva_warmup() (cobra.flux_analysis.sampling.HRSampler method)
genes (cobra.core.model.Model attribute)
genes() (cobra.core.reaction.Reaction method)
geometric_fba() (in module cobra.flux_analysis.geometric)
get_attrib() (in module cobra.io.sbml3)
get_by_any() (cobra.core.dictlist.DictList method)
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_compiled_gene_reaction_rules() (in module cobra.manipulation.delete)
get_context() (in module cobra.util.context)
get_ids() (in module cobra.test.test_io_order)
get_libsbml_document() (in module cobra.io.sbml)
get_metabolite_compartments() (cobra.core.model.Model method)
get_solution() (in module cobra.core.solution)
get_solver_name() (in module cobra.util.solver)
GPRCleaner (class in cobra.core.gene)
H
has_id() (cobra.core.dictlist.DictList method)
HistoryManager (class in cobra.util.context)
HRSampler (class in cobra.flux_analysis.sampling)
I
id() (cobra.core.object.Object method)
,
[1]
indent_xml() (in module cobra.io.sbml3)
index() (cobra.core.dictlist.DictList method)
Infeasible (class in cobra.exceptions)
insert() (cobra.core.dictlist.DictList method)
insert_break() (in module scripts.publish_release)
interface_to_str() (in module cobra.util.solver)
intify() (in module scripts.publish_release)
io_trial() (in module cobra.test.test_io)
is_boundary_type() (in module cobra.medium.boundary_types)
K
knock_out() (cobra.core.gene.Gene method)
(cobra.core.reaction.Reaction method)
L
large_model() (in module cobra.test.conftest)
large_once() (in module cobra.test.conftest)
LegacySolution (class in cobra.core.solution)
linear_reaction_coefficients() (in module cobra.util.solver)
list_attr() (cobra.core.dictlist.DictList method)
ll_test_model() (in module cobra.test.test_flux_analysis)
load_json_model() (in module cobra.io.json)
load_matlab_model() (in module cobra.io.mat)
load_yaml_model() (in module cobra.io.yaml)
loopless_fva_iter() (in module cobra.flux_analysis.loopless)
loopless_solution() (in module cobra.flux_analysis.loopless)
lower_bound() (cobra.core.reaction.Reaction method)
,
[1]
M
main() (in module scripts.publish_release)
make_plot_ax() (in module documentation_builder.plot_helper)
medium() (cobra.core.model.Model method)
,
[1]
medium_model() (in module cobra.test.conftest)
merge() (cobra.core.model.Model method)
Metabolite (class in cobra.core.metabolite)
metabolite_from_dict() (in module cobra.io.dict)
metabolite_summary() (in module cobra.flux_analysis.summary)
metabolite_to_dict() (in module cobra.io.dict)
metabolites (cobra.core.model.Model attribute)
metabolites() (cobra.core.reaction.Reaction method)
(in module cobra.test.conftest)
minimal_medium() (in module cobra.medium.minimal_medium)
minimized_reverse() (in module cobra.test.test_io_order)
minimized_shuffle() (in module cobra.test.test_io_order)
minimized_sorted() (in module cobra.test.test_io_order)
Mock (class in documentation_builder.conf)
Model (class in cobra.core.model)
model (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
model() (cobra.core.reaction.Reaction method)
(cobra.core.species.Species method)
(in module cobra.test.conftest)
model_from_dict() (in module cobra.io.dict)
model_summary() (in module cobra.flux_analysis.summary)
model_to_dict() (in module cobra.io.dict)
model_to_pymatbridge() (in module cobra.io.mat)
model_to_xml() (in module cobra.io.sbml3)
moma() (in module cobra.flux_analysis.moma)
mp_init() (in module cobra.flux_analysis.sampling)
N
n_samples (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
nproj (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
ns() (in module cobra.io.sbml3)
nullspace() (in module cobra.util.array)
O
Object (class in cobra.core.object)
objective() (cobra.core.model.Model method)
,
[1]
objective_coefficient() (cobra.core.reaction.Reaction method)
,
[1]
objective_direction() (cobra.core.model.Model method)
,
[1]
objective_value (cobra.core.solution.Solution attribute)
opt_solver() (in module cobra.test.conftest)
OptGPSampler (class in cobra.flux_analysis.sampling)
OptimizationError (class in cobra.exceptions)
optimize() (cobra.core.model.Model method)
optimize_minimal_flux() (in module cobra.flux_analysis.parsimonious)
P
parse_composition() (cobra.core.formula.Formula method)
parse_gpr() (in module cobra.core.gene)
parse_legacy_id() (in module cobra.io.sbml)
parse_legacy_sbml_notes() (in module cobra.io.sbml)
parse_stream() (in module cobra.io.sbml3)
parse_xml_into_model() (in module cobra.io.sbml3)
pfba() (in module cobra.flux_analysis.parsimonious)
pfba_fva_results() (in module cobra.test.conftest)
plot_loop() (in module documentation_builder.plot_helper)
plot_qp1() (in module documentation_builder.plot_helper)
plot_qp2() (in module documentation_builder.plot_helper)
pop() (cobra.core.dictlist.DictList method)
prev (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
problem (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
problem() (cobra.core.model.Model method)
production_envelope() (in module cobra.flux_analysis.phenotype_phase_plane)
products() (cobra.core.reaction.Reaction method)
prune_unused_metabolites() (in module cobra.manipulation.delete)
prune_unused_reactions() (in module cobra.manipulation.delete)
pytest_addoption() (in module cobra.test.conftest)
Q
query() (cobra.core.dictlist.DictList method)
R
raise_libsbml_errors() (in module cobra.test.test_io)
raise_scipy_errors() (in module cobra.test.test_io)
reactants() (cobra.core.reaction.Reaction method)
Reaction (class in cobra.core.reaction)
reaction() (cobra.core.reaction.Reaction method)
,
[1]
reaction_elements() (in module cobra.flux_analysis.phenotype_phase_plane)
reaction_from_dict() (in module cobra.io.dict)
reaction_to_dict() (in module cobra.io.dict)
reaction_weight() (in module cobra.flux_analysis.phenotype_phase_plane)
reactions (cobra.core.model.Model attribute)
reactions() (cobra.core.species.Species method)
read_legacy_sbml() (in module cobra.io.sbml)
read_pickle() (in module cobra.test.test_io)
read_sbml_model() (in module cobra.io.sbml3)
reduced_cost() (cobra.core.reaction.Reaction method)
reduced_costs (cobra.core.solution.Solution attribute)
remove() (cobra.core.dictlist.DictList method)
remove_cons_vars() (cobra.core.model.Model method)
remove_cons_vars_from_problem() (in module cobra.util.solver)
remove_from_model() (cobra.core.gene.Gene method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.reaction.Reaction method)
remove_genes() (in module cobra.manipulation.delete)
remove_metabolites() (cobra.core.model.Model method)
remove_reactions() (cobra.core.model.Model method)
rename_genes() (in module cobra.manipulation.modify)
repair() (cobra.core.model.Model method)
reset() (cobra.util.context.HistoryManager method)
resettable() (in module cobra.util.context)
retries (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
rev_idx (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
reverse() (cobra.core.dictlist.DictList method)
reverse_id() (cobra.core.reaction.Reaction method)
reverse_variable() (cobra.core.reaction.Reaction method)
reversibility() (cobra.core.reaction.Reaction method)
,
[1]
revert_to_reversible() (in module cobra.manipulation.modify)
room() (in module cobra.flux_analysis.room)
S
salmonella() (in module cobra.test.conftest)
same_ex() (in module cobra.test.test_solver_model)
sample() (cobra.flux_analysis.sampling.ACHRSampler method)
(cobra.flux_analysis.sampling.HRSampler method)
(cobra.flux_analysis.sampling.OptGPSampler method)
(in module cobra.flux_analysis.sampling)
save_json_model() (in module cobra.io.json)
save_matlab_model() (in module cobra.io.mat)
save_yaml_model() (in module cobra.io.yaml)
scripts.compare-benchmark (module)
scripts.publish_release (module)
seed (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
separate_forward_and_reverse_bounds() (in module cobra.core.reaction)
set_attrib() (in module cobra.io.sbml3)
set_objective() (in module cobra.util.solver)
setup_class() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
shadow_price() (cobra.core.metabolite.Metabolite method)
shadow_prices (cobra.core.solution.Solution attribute)
shared_np_array() (in module cobra.flux_analysis.sampling)
show_versions() (in module cobra.util.util)
single_gene_deletion() (in module cobra.flux_analysis.deletion)
single_reaction_deletion() (in module cobra.flux_analysis.deletion)
sinks() (cobra.core.model.Model method)
slim_optimize() (cobra.core.model.Model method)
small_model() (in module cobra.test.conftest)
Solution (class in cobra.core.solution)
solution (cobra.core.model.Model attribute)
solved_model() (in module cobra.test.conftest)
(in module cobra.test.test_solver_model)
solver (cobra.core.solution.LegacySolution attribute)
solver() (cobra.core.model.Model method)
,
[1]
SolverNotFound (class in cobra.exceptions)
sort() (cobra.core.dictlist.DictList method)
Species (class in cobra.core.species)
status (cobra.core.solution.Solution attribute)
strnum() (in module cobra.io.sbml3)
subtract_metabolites() (cobra.core.reaction.Reaction method)
summary() (cobra.core.metabolite.Metabolite method)
(cobra.core.model.Model method)
T
template() (in module cobra.test.test_io_order)
test_absolute_expression() (cobra.test.test_solver_utils.TestSolverMods method)
test_achr_init_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_achr_sample_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_add() (cobra.test.test_model.TestReactions method)
(cobra.test.test_util.TestDictList method)
test_add_boundary() (cobra.test.test_model.TestCobraModel method)
test_add_boundary_context() (cobra.test.test_model.TestCobraModel method)
test_add_cobra_reaction() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_add_existing_boundary() (cobra.test.test_model.TestCobraModel method)
test_add_loopless() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_add_metabolite() (cobra.test.test_model.TestCobraModel method)
(cobra.test.test_model.TestReactions method)
(cobra.test.test_solver_model.TestReaction method)
test_add_metabolite_benchmark() (cobra.test.test_model.TestReactions method)
test_add_metabolites_combine_false() (cobra.test.test_solver_model.TestReaction method)
test_add_metabolites_combine_true() (cobra.test.test_solver_model.TestReaction method)
test_add_reaction() (cobra.test.test_model.TestCobraModel method)
test_add_reaction_context() (cobra.test.test_model.TestCobraModel method)
test_add_reaction_from_other_model() (cobra.test.test_model.TestCobraModel method)
test_add_reaction_orphans() (cobra.test.test_model.TestCobraModel method)
test_add_reactions() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_add_reactions_duplicate() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_add_reactions_single_existing() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_add_remove() (cobra.test.test_solver_utils.TestSolverMods method)
test_add_remove_in_context() (cobra.test.test_solver_utils.TestSolverMods method)
test_add_remove_reaction_benchmark() (cobra.test.test_model.TestCobraModel method)
test_all() (in module cobra.test)
test_all_objects_point_to_all_other_correct_objects() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_append() (cobra.test.test_util.TestDictList method)
test_assess() (cobra.test.test_flux_analysis.TestReactionUtils method)
test_bad_validation() (in module cobra.test.test_io)
test_batch_sampling() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_benchmark_medium_linear() (cobra.test.test_medium.TestMinimalMedia method)
test_benchmark_medium_mip() (cobra.test.test_medium.TestMinimalMedia method)
test_benchmark_read() (in module cobra.test.test_io)
test_benchmark_write() (in module cobra.test.test_io)
test_bounds_setter() (cobra.test.test_model.TestReactions method)
test_build_from_string() (cobra.test.test_model.TestReactions method)
test_change_bounds() (cobra.test.test_solver_model.TestReaction method)
test_change_id_is_reflected_in_solver() (cobra.test.test_solver_model.TestReaction method)
test_change_objective() (cobra.test.test_model.TestCobraModel method)
(cobra.test.test_solver_model.TestSolverBasedModel method)
test_change_objective_benchmark() (cobra.test.test_model.TestCobraModel method)
test_change_objective_through_objective_coefficient() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_change_solver_to_cplex_and_check_copy_works() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_choose_solver() (cobra.test.test_solver_utils.TestHelpers method)
test_compartments() (cobra.test.test_model.TestCobraModel method)
test_complicated_model() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_contains() (cobra.test.test_util.TestDictList method)
test_context_manager() (cobra.test.test_model.TestCobraModel method)
test_copy() (cobra.test.test_model.TestCobraModel method)
(cobra.test.test_model.TestReactions method)
(cobra.test.test_util.TestDictList method)
test_copy_benchmark() (cobra.test.test_model.TestCobraModel method)
test_copy_benchmark_large_model() (cobra.test.test_model.TestCobraModel method)
test_copy_preserves_existing_solution() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_deepcopy() (cobra.test.test_model.TestCobraModel method)
(cobra.test.test_util.TestDictList method)
test_deepcopy_benchmark() (cobra.test.test_model.TestCobraModel method)
test_demand() (cobra.test.test_medium.TestTypeDetection method)
test_dense_matrix() (cobra.test.test_model.TestStoichiometricMatrix method)
test_dir() (cobra.test.test_util.TestDictList method)
test_double_gene_deletion() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_double_gene_deletion_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_double_reaction_deletion() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_double_reaction_deletion_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_envelope_multi_reaction_objective() (cobra.test.test_flux_analysis.TestProductionEnvelope method)
test_envelope_one() (cobra.test.test_flux_analysis.TestProductionEnvelope method)
test_envelope_two() (cobra.test.test_flux_analysis.TestProductionEnvelope method)
test_equality_constraint() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_escape_ids() (cobra.test.test_manipulation.TestManipulation method)
test_essential_genes() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_essential_reactions() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_exchange() (cobra.test.test_medium.TestTypeDetection method)
test_exchange_reactions() (cobra.test.test_model.TestCobraModel method)
test_extend() (cobra.test.test_util.TestDictList method)
test_external_compartment() (cobra.test.test_medium.TestTypeDetection method)
test_fail_non_linear_reaction_coefficients() (cobra.test.test_solver_utils.TestObjectiveHelpers method)
test_find_blocked_reactions() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_find_blocked_reactions_solver_none() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_fix_objective_as_constraint() (cobra.test.test_solver_utils.TestSolverMods method)
test_fix_objective_as_constraint_minimize() (cobra.test.test_solver_utils.TestSolverMods method)
test_fixed_seed() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_flux_variability() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_flux_variability_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_flux_variability_loopless() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_flux_variability_loopless_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_formula_element_setting() (cobra.test.test_model.TestCobraMetabolites method)
test_fva_data_frame() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_fva_infeasible() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_fva_minimization() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_gapfilling() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_gene_knock_out() (cobra.test.test_model.TestReactions method)
test_gene_knockout_computation() (cobra.test.test_manipulation.TestManipulation method)
test_geometric_fba() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_geometric_fba_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_get_by_any() (cobra.test.test_util.TestDictList method)
test_get_objective_direction() (cobra.test.test_model.TestCobraModel method)
test_gpr() (cobra.test.test_model.TestReactions method)
test_gpr_modification() (cobra.test.test_model.TestReactions method)
test_iadd() (cobra.test.test_model.TestReactions method)
(cobra.test.test_util.TestDictList method)
test_independent() (cobra.test.test_util.TestDictList method)
test_index() (cobra.test.test_util.TestDictList method)
test_inequality_constraint() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_inhomogeneous_sanity() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_init_copy() (cobra.test.test_util.TestDictList method)
test_insert() (cobra.test.test_util.TestDictList method)
test_interface_str() (cobra.test.test_solver_utils.TestHelpers method)
test_invalid_objective_raises() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_invalid_solver_change_raises() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_io_order() (in module cobra.test.test_io_order)
test_irrev_reaction_set_negative_lb() (cobra.test.test_solver_model.TestReaction method)
test_isub() (cobra.test.test_util.TestDictList method)
test_knockout() (cobra.test.test_solver_model.TestReaction method)
test_linear_moma_sanity() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_linear_reaction_coefficients() (cobra.test.test_solver_utils.TestObjectiveHelpers method)
test_linear_room_sanity() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_loopless_benchmark_after() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_loopless_benchmark_before() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_loopless_solution() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_loopless_solution_fluxes() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_make_irreversible() (cobra.test.test_solver_model.TestReaction method)
test_make_irreversible_irreversible_to_the_other_side() (cobra.test.test_solver_model.TestReaction method)
test_make_lhs_irreversible_reversible() (cobra.test.test_solver_model.TestReaction method)
test_make_reversible() (cobra.test.test_solver_model.TestReaction method)
test_mass_balance() (cobra.test.test_model.TestReactions method)
test_medium_alternative_mip() (cobra.test.test_medium.TestMinimalMedia method)
test_medium_exports() (cobra.test.test_medium.TestMinimalMedia method)
test_medium_linear() (cobra.test.test_medium.TestMinimalMedia method)
test_medium_mip() (cobra.test.test_medium.TestMinimalMedia method)
test_merge_models() (cobra.test.test_model.TestCobraModel method)
test_metabolite_formula() (cobra.test.test_model.TestCobraMetabolites method)
test_metabolite_summary() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_metabolite_summary_previous_solution() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_metabolite_summary_with_fva() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_model_from_other_model() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_model_less_reaction() (cobra.test.test_solver_model.TestReaction method)
test_model_medium() (cobra.test.test_medium.TestModelMedium method)
test_model_remove_reaction() (cobra.test.test_model.TestCobraModel method)
test_model_summary() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_model_summary_previous_solution() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_model_summary_with_fva() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_modify_reversible() (cobra.test.test_manipulation.TestManipulation method)
test_moma_sanity() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_mul() (cobra.test.test_model.TestReactions method)
test_multi_optgp() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_multi_variable_envelope() (cobra.test.test_flux_analysis.TestProductionEnvelope method)
test_no_boundary_reactions() (cobra.test.test_medium.TestErrorsAndExceptions method)
,
[1]
test_no_change_for_same_solver() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_objective() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_objective_coefficient_reflects_changed_objective() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_objects_point_to_correct_other_after_copy() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_one_left_to_right_reaction_set_positive_ub() (cobra.test.test_solver_model.TestReaction method)
test_open_exchanges() (cobra.test.test_medium.TestMinimalMedia method)
test_optgp_init_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_optgp_sample_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_optimize() (cobra.test.test_model.TestCobraModel method)
test_pfba() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_pfba_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_pfba_flux_variability() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_pickle() (cobra.test.test_util.TestDictList method)
test_problem_properties() (cobra.test.test_model.TestCobraModel method)
test_prune_unused() (cobra.test.test_manipulation.TestManipulation method)
test_query() (cobra.test.test_util.TestDictList method)
test_radd() (cobra.test.test_model.TestReactions method)
test_reaction_delete() (cobra.test.test_model.TestCobraModel method)
test_reaction_imul() (cobra.test.test_solver_model.TestReaction method)
test_reaction_remove() (cobra.test.test_model.TestCobraModel method)
test_reaction_without_model() (cobra.test.test_solver_model.TestReaction method)
test_read_1() (cobra.test.test_io.TestCobraIO method)
test_read_2() (cobra.test.test_io.TestCobraIO method)
test_read_nonexistent() (in module cobra.test.test_io)
test_removal() (cobra.test.test_util.TestDictList method)
test_removal_from_model_retains_bounds() (cobra.test.test_solver_model.TestReaction method)
test_remove_from_model() (cobra.test.test_solver_model.TestMetabolite method)
(cobra.test.test_solver_model.TestReaction method)
test_remove_gene() (cobra.test.test_model.TestCobraModel method)
test_remove_genes() (cobra.test.test_manipulation.TestManipulation method)
test_remove_metabolite_destructive() (cobra.test.test_model.TestCobraModel method)
test_remove_metabolite_subtractive() (cobra.test.test_model.TestCobraModel method)
test_remove_reactions() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_rename_gene() (cobra.test.test_manipulation.TestManipulation method)
test_repr_html_() (cobra.test.test_model.TestCobraGenes method)
(cobra.test.test_model.TestCobraMetabolites method)
(cobra.test.test_model.TestCobraModel method)
(cobra.test.test_model.TestReactions method)
test_reproject() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_room_sanity() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_sampling() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_sbml_error() (in module cobra.test.test_io)
test_sbo_annotation() (cobra.test.test_manipulation.TestManipulation method)
test_sbo_terms() (cobra.test.test_medium.TestTypeDetection method)
test_set() (cobra.test.test_util.TestDictList method)
test_set_bounds_scenario_1() (cobra.test.test_solver_model.TestReaction method)
test_set_bounds_scenario_2() (cobra.test.test_solver_model.TestReaction method)
test_set_bounds_scenario_3() (cobra.test.test_solver_model.TestReaction method)
test_set_bounds_scenario_4() (cobra.test.test_solver_model.TestReaction method)
test_set_id() (cobra.test.test_solver_model.TestMetabolite method)
test_set_lb_higher_than_ub_sets_ub_to_new_lb() (cobra.test.test_solver_model.TestReaction method)
test_set_objective_direction() (cobra.test.test_model.TestCobraModel method)
test_set_reaction_objective() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_set_reaction_objective_str() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_set_ub_lower_than_lb_sets_lb_to_new_ub() (cobra.test.test_solver_model.TestReaction method)
test_set_upper_before_lower_bound_to_0() (cobra.test.test_solver_model.TestReaction method)
test_show_versions() (in module cobra.test.test_util)
test_single_achr() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_single_gene_deletion_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_fba() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_fba_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_linear_moma() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_linear_moma_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_linear_room_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_moma() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_moma_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_moma_reference() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_gene_deletion_room_benchmark() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_optgp() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_single_point_space() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_single_reaction_deletion() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_reaction_deletion_room() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_single_reaction_deletion_room_linear() (cobra.test.test_flux_analysis.TestCobraFluxAnalysis method)
test_sink() (cobra.test.test_medium.TestTypeDetection method)
test_slice() (cobra.test.test_util.TestDictList method)
test_slim_optimize() (cobra.test.test_model.TestCobraModel method)
test_solution_contains_only_reaction_specific_values() (cobra.test.test_solver_model.TestSolution method)
test_solution_data_frame() (cobra.test.test_model.TestCobraModel method)
test_solver_change() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_solver_list() (cobra.test.test_solver_utils.TestHelpers method)
test_solver_name() (cobra.test.test_solver_utils.TestHelpers method)
test_sort_and_reverse() (cobra.test.test_util.TestDictList method)
test_sparse_matrix() (cobra.test.test_model.TestStoichiometricMatrix method)
test_str() (cobra.test.test_model.TestReactions method)
(cobra.test.test_solver_model.TestReaction method)
test_sub() (cobra.test.test_model.TestReactions method)
(cobra.test.test_util.TestDictList method)
test_subtract_metabolite() (cobra.test.test_model.TestReactions method)
test_subtract_metabolite_benchmark() (cobra.test.test_model.TestReactions method)
test_transfer_objective() (cobra.test.test_solver_model.TestSolverBasedModel method)
test_twist_irrev_right_to_left_reaction_to_left_to_right() (cobra.test.test_solver_model.TestReaction method)
test_union() (cobra.test.test_util.TestDictList method)
test_validate() (in module cobra.test.test_io)
test_validate_formula_compartment() (cobra.test.test_manipulation.TestManipulation method)
test_validate_mass_balance() (cobra.test.test_manipulation.TestManipulation method)
test_validate_wrong_sample() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_variables_samples() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
test_weird_left_to_right_reaction_issue() (cobra.test.test_solver_model.TestReaction method)
test_write_1() (cobra.test.test_io.TestCobraIO method)
test_write_2() (cobra.test.test_io.TestCobraIO method)
test_wrong_method() (cobra.test.test_flux_analysis.TestCobraFluxSampling method)
TestCobraFluxAnalysis (class in cobra.test.test_flux_analysis)
TestCobraFluxSampling (class in cobra.test.test_flux_analysis)
TestCobraGenes (class in cobra.test.test_model)
TestCobraIO (class in cobra.test.test_io)
TestCobraMetabolites (class in cobra.test.test_model)
TestCobraModel (class in cobra.test.test_model)
TestDictList (class in cobra.test.test_util)
TestErrorsAndExceptions (class in cobra.test.test_medium)
TestHelpers (class in cobra.test.test_solver_utils)
TestManipulation (class in cobra.test.test_manipulation)
TestMetabolite (class in cobra.test.test_solver_model)
TestMinimalMedia (class in cobra.test.test_medium)
TestModelMedium (class in cobra.test.test_medium)
TestObjectiveHelpers (class in cobra.test.test_solver_utils)
TestProductionEnvelope (class in cobra.test.test_flux_analysis)
TestReaction (class in cobra.test.test_solver_model)
TestReactions (class in cobra.test.test_model)
TestReactionUtils (class in cobra.test.test_flux_analysis)
TestSolution (class in cobra.test.test_solver_model)
TestSolverBasedModel (class in cobra.test.test_solver_model)
TestSolverMods (class in cobra.test.test_solver_utils)
TestStoichiometricMatrix (class in cobra.test.test_model)
TestTypeDetection (class in cobra.test.test_medium)
thinning (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
tiny_toy_model() (in module cobra.test.conftest)
tmp_path() (in module cobra.test.test_io_order)
to_frame() (cobra.core.solution.Solution method)
to_json() (in module cobra.io.json)
to_yaml() (in module cobra.io.yaml)
total_components_flux() (in module cobra.flux_analysis.phenotype_phase_plane)
total_yield() (in module cobra.flux_analysis.phenotype_phase_plane)
U
Unbounded (class in cobra.exceptions)
UndefinedSolution (class in cobra.exceptions)
undelete_model_genes() (in module cobra.manipulation.delete)
union() (cobra.core.dictlist.DictList method)
update_costs() (cobra.flux_analysis.gapfilling.GapFiller method)
update_forward_and_reverse_bounds() (in module cobra.core.reaction)
upper_bound() (cobra.core.reaction.Reaction method)
,
[1]
V
validate() (cobra.flux_analysis.gapfilling.GapFiller method)
(cobra.flux_analysis.sampling.HRSampler method)
validate_json() (in module cobra.test.test_io)
validate_sbml_model() (in module cobra.io.sbml3)
variables() (cobra.core.model.Model method)
visit_BinOp() (cobra.core.gene.GPRCleaner method)
visit_BoolOp() (cobra.manipulation.delete._GeneRemover method)
visit_Name() (cobra.core.gene.GPRCleaner method)
(cobra.manipulation.delete._GeneRemover method)
(cobra.manipulation.modify._GeneEscaper method)
W
warmup (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
weight() (cobra.core.formula.Formula method)
write_cobra_model_to_sbml_file() (in module cobra.io.sbml)
write_legacy_sbml_placeholder() (in module cobra.test.test_io)
write_pickle() (in module cobra.test.test_io)
write_sbml_model() (in module cobra.io.sbml3)
X
x (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
x() (cobra.core.reaction.Reaction method)
(cobra.core.solution.Solution method)
x_dict (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
x_dict() (cobra.core.solution.Solution method)
,
[1]
Y
y (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
y() (cobra.core.metabolite.Metabolite method)
(cobra.core.reaction.Reaction method)
(cobra.core.solution.Solution method)
y_dict (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
y_dict() (cobra.core.solution.Solution method)
,
[1]
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