cobra
0.19.0
1. Global Configuration
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. Consistency testing
10. Gapfillling
11. Growth media
12. Solvers
13. Tailored constraints, variables and objectives
14. Dynamic Flux Balance Analysis (dFBA) in COBRApy
15. Using the COBRA toolbox with cobrapy
16. FAQ
17. API Reference
cobra
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
_
__add__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.formula.Formula method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__author__ (in module cobra)
__build_problem() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
__call__() (cobra.core.singleton.Singleton method)
(cobra.util.context.HistoryManager method)
(cobra.util.HistoryManager method)
__contains__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__copy__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__deepcopy__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__delitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__delslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__dir__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__enter__() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
__exit__() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
__getattr__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__getitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.LegacySolution method)
(cobra.core.Solution method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.DictList method)
(cobra.flux_analysis.deletion.KnockoutAccessor method)
(cobra.Solution method)
(cobra.util.AutoVivification method)
(cobra.util.util.AutoVivification method)
__getslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__getstate__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Species method)
(cobra.core.species.Species method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Object method)
(cobra.sampling.optgp.OptGPSampler method)
(cobra.sampling.OptGPSampler method)
(cobra.Species method)
__iadd__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__imul__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__isub__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__len__() (cobra.core.Group method)
(cobra.core.group.Group method)
__mul__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__radd__ (cobra.core.Reaction attribute)
(cobra.core.reaction.Reaction attribute)
(cobra.Reaction attribute)
__reduce__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__repr__() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
(cobra.core.LegacySolution method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Solution method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.Object method)
(cobra.Solution method)
__setitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__setslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__setstate__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__single_iteration() (cobra.sampling.achr.ACHRSampler method)
(cobra.sampling.ACHRSampler method)
__str__() (cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Object method)
(cobra.Reaction method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
__sub__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__version__ (in module cobra)
_add_cycle_free() (in module cobra.flux_analysis.loopless)
_as_medium() (in module cobra.medium.minimal_medium)
_associate_gene() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_bounds_dist() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_bracket_re (in module cobra.io.mat)
_cell() (in module cobra.io.mat)
_check() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
(in module cobra.io.mat)
(in module cobra.io.sbml)
_check_bounds() (cobra.core.Reaction static method)
(cobra.core.reaction.Reaction static method)
(cobra.Reaction static method)
_check_required() (in module cobra.io.sbml)
_check_sbml_annotations() (in module cobra.test.test_io.test_annotation)
_clip() (in module cobra.io.sbml)
_create_bound() (in module cobra.io.sbml)
_create_parameter() (in module cobra.io.sbml)
_display_flux() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
_dissociate_gene() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_element_lists() (in module cobra.flux_analysis.deletion)
_entities_ids() (in module cobra.flux_analysis.deletion)
_error_string() (in module cobra.io.sbml)
_escape_non_alphanum() (in module cobra.io.sbml)
_escape_str_id() (in module cobra.manipulation.modify)
_extend_nocheck() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_f_gene() (in module cobra.io.sbml)
_f_gene_rev() (in module cobra.io.sbml)
_f_group() (in module cobra.io.sbml)
_f_group_rev() (in module cobra.io.sbml)
_f_reaction() (in module cobra.io.sbml)
_f_reaction_rev() (in module cobra.io.sbml)
_f_specie() (in module cobra.io.sbml)
_f_specie_rev() (in module cobra.io.sbml)
_find_sparse_mode() (in module cobra.flux_analysis.fastcc)
_fix_type() (in module cobra.io.dict)
_flip_coefficients() (in module cobra.flux_analysis.fastcc)
_forward_arrow_finder (in module cobra.core.reaction)
_fva_step() (in module cobra.flux_analysis.variability)
_gene_deletion() (in module cobra.flux_analysis.deletion)
_gene_deletion_worker() (in module cobra.flux_analysis.deletion)
_GeneEscaper (class in cobra.manipulation.modify)
_generate() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_generate_index() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_GeneRemover (class in cobra.manipulation.delete)
_get_doc_from_filename() (in module cobra.io.sbml)
_get_growth() (in module cobra.flux_analysis.deletion)
_get_id_compartment() (in module cobra.io.mat)
_html_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method)
(cobra.summary.MetaboliteSummary static method)
(cobra.summary.model_summary.ModelSummary static method)
(cobra.summary.ModelSummary static method)
_init_worker() (in module cobra.flux_analysis.deletion)
(in module cobra.flux_analysis.variability)
_instances (cobra.core.singleton.Singleton attribute)
_is_redundant() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_model_to_sbml() (in module cobra.io.sbml)
_multi_deletion() (in module cobra.flux_analysis.deletion)
_normalize_threshold() (cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_number_to_chr() (in module cobra.io.sbml)
_optimize_or_value() (in module cobra.flux_analysis.reaction)
_OPTIONAL_GENE_ATTRIBUTES (in module cobra.io.dict)
_OPTIONAL_METABOLITE_ATTRIBUTES (in module cobra.io.dict)
_OPTIONAL_MODEL_ATTRIBUTES (in module cobra.io.dict)
_OPTIONAL_REACTION_ATTRIBUTES (in module cobra.io.dict)
_ORDERED_OPTIONAL_GENE_KEYS (in module cobra.io.dict)
_ORDERED_OPTIONAL_METABOLITE_KEYS (in module cobra.io.dict)
_ORDERED_OPTIONAL_MODEL_KEYS (in module cobra.io.dict)
_ORDERED_OPTIONAL_REACTION_KEYS (in module cobra.io.dict)
_parse_annotation_info() (in module cobra.io.sbml)
_parse_annotations() (in module cobra.io.sbml)
_parse_notes_dict() (in module cobra.io.sbml)
_populate_solver() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
_random_point() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.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)
_renames (in module cobra.manipulation.modify)
_replace_on_id() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_repr_html_() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
(cobra.core.Gene method)
(cobra.core.gene.Gene method)
(cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.core.Solution method)
(cobra.core.solution.Solution method)
(cobra.Gene method)
(cobra.Metabolite method)
(cobra.Model method)
(cobra.Reaction method)
(cobra.Solution method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_reproject() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_REQUIRED_GENE_ATTRIBUTES (in module cobra.io.dict)
_REQUIRED_METABOLITE_ATTRIBUTES (in module cobra.io.dict)
_REQUIRED_REACTION_ATTRIBUTES (in module cobra.io.dict)
_reverse_arrow_finder (in module cobra.core.reaction)
_reversible_arrow_finder (in module cobra.core.reaction)
_sbase_annotations() (in module cobra.io.sbml)
_sbase_notes_dict() (in module cobra.io.sbml)
_sbml_to_model() (in module cobra.io.sbml)
_set_default_processes() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
_set_default_solver() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
_set_id_with_model() (cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Metabolite method)
(cobra.Object method)
(cobra.Reaction method)
_string_flux() (cobra.summary.reaction_summary.ReactionSummary method)
_string_objective() (cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
_string_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method)
(cobra.summary.MetaboliteSummary static method)
(cobra.summary.model_summary.ModelSummary static method)
(cobra.summary.ModelSummary static method)
_underscore_re (in module cobra.io.mat)
_update_awareness() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_update_optional() (in module cobra.io.dict)
_valid_atoms() (in module cobra.util)
(in module cobra.util.solver)
_validate() (cobra.flux_analysis.deletion.KnockoutAccessor static method)
A
achr() (in module cobra.test.test_sampling.conftest)
ACHRSampler (class in cobra.sampling)
(class in cobra.sampling.achr)
add() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
add_absolute_expression() (in module cobra.util)
(in module cobra.util.solver)
add_boundary() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_cons_vars() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_cons_vars_to_problem() (in module cobra.util)
(in module cobra.util.solver)
add_envelope() (in module cobra.flux_analysis.phenotype_phase_plane)
add_groups() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_lexicographic_constraints() (in module cobra.util)
(in module cobra.util.solver)
add_linear_obj() (in module cobra.medium.minimal_medium)
add_loopless() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.loopless)
add_lp_feasibility() (in module cobra.util)
(in module cobra.util.solver)
add_members() (cobra.core.Group method)
(cobra.core.group.Group method)
add_metabolites() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Model method)
(cobra.Reaction method)
add_mip_obj() (in module cobra.medium.minimal_medium)
add_moma() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.moma)
add_pfba() (in module cobra.flux_analysis.parsimonious)
add_reaction() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_reactions() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
add_room() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.room)
add_SBO() (in module cobra.manipulation)
(in module cobra.manipulation.annotate)
add_switches_and_objective() (cobra.flux_analysis.gapfilling.GapFiller method)
all_solvers (in module cobra.test.conftest)
all_solvers() (in module cobra.test.test_flux_analysis.conftest)
and_or_search (in module cobra.core.reaction)
annotation() (cobra.core.Object property)
(cobra.core.object.Object property)
(cobra.Object property)
append() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
assert_optimal() (in module cobra.util)
(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.test_io_order)
AutoVivification (class in cobra.util)
(class in cobra.util.util)
B
b (in module cobra.sampling.hr_sampler)
batch() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
BOUND_MINUS_INF (in module cobra.io.sbml)
BOUND_PLUS_INF (in module cobra.io.sbml)
boundary() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Model property)
(cobra.Reaction property)
bounds (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(in module cobra.sampling.hr_sampler)
bounds() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
bounds_tol (cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
build_reaction_from_string() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
build_reaction_string() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
C
center (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
check_mass_balance() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
(in module cobra.manipulation)
(in module cobra.manipulation.validate)
check_metabolite_compartment_formula() (in module cobra.manipulation)
(in module cobra.manipulation.validate)
check_solver_status() (in module cobra.util)
(in module cobra.util.solver)
choose_solver() (in module cobra.util)
(in module cobra.util.solver)
clean_result (in module cobra.test.data.update_pickles)
,
[1]
cload (in module cobra.test.test_io.test_pickle)
cobra (module)
cobra.core (module)
cobra.core.configuration (module)
cobra.core.dictlist (module)
cobra.core.formula (module)
cobra.core.gene (module)
cobra.core.group (module)
cobra.core.metabolite (module)
cobra.core.model (module)
cobra.core.object (module)
cobra.core.reaction (module)
cobra.core.singleton (module)
cobra.core.solution (module)
cobra.core.species (module)
cobra.exceptions (module)
cobra.flux_analysis (module)
cobra.flux_analysis.deletion (module)
cobra.flux_analysis.fastcc (module)
cobra.flux_analysis.gapfilling (module)
cobra.flux_analysis.geometric (module)
cobra.flux_analysis.helpers (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.variability (module)
cobra.io (module)
cobra.io.dict (module)
cobra.io.json (module)
cobra.io.mat (module)
cobra.io.sbml (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.annotations (module)
cobra.medium.boundary_types (module)
cobra.medium.minimal_medium (module)
cobra.sampling (module)
cobra.sampling.achr (module)
cobra.sampling.hr_sampler (module)
cobra.sampling.optgp (module)
cobra.sampling.sampling (module)
cobra.summary (module)
cobra.summary.metabolite_summary (module)
cobra.summary.model_summary (module)
cobra.summary.reaction_summary (module)
cobra.summary.summary (module)
cobra.test (module)
cobra.test.conftest (module)
cobra.test.data (module)
cobra.test.data.update_pickles (module)
cobra.test.test_core (module)
cobra.test.test_core.conftest (module)
cobra.test.test_core.test_configuration (module)
cobra.test.test_core.test_core_reaction (module)
cobra.test.test_core.test_dictlist (module)
cobra.test.test_core.test_gene (module)
cobra.test.test_core.test_group (module)
cobra.test.test_core.test_metabolite (module)
cobra.test.test_core.test_model (module)
cobra.test.test_core.test_solution (module)
cobra.test.test_flux_analysis (module)
cobra.test.test_flux_analysis.conftest (module)
cobra.test.test_flux_analysis.test_deletion (module)
cobra.test.test_flux_analysis.test_fastcc (module)
cobra.test.test_flux_analysis.test_gapfilling (module)
cobra.test.test_flux_analysis.test_geometric (module)
cobra.test.test_flux_analysis.test_loopless (module)
cobra.test.test_flux_analysis.test_moma (module)
cobra.test.test_flux_analysis.test_parsimonious (module)
cobra.test.test_flux_analysis.test_phenotype_phase_plane (module)
cobra.test.test_flux_analysis.test_reaction (module)
cobra.test.test_flux_analysis.test_room (module)
cobra.test.test_flux_analysis.test_variability (module)
cobra.test.test_io (module)
cobra.test.test_io.conftest (module)
cobra.test.test_io.test_annotation (module)
cobra.test.test_io.test_annotation_format (module)
cobra.test.test_io.test_io_order (module)
cobra.test.test_io.test_json (module)
cobra.test.test_io.test_mat (module)
cobra.test.test_io.test_notes (module)
cobra.test.test_io.test_pickle (module)
cobra.test.test_io.test_sbml (module)
cobra.test.test_io.test_yaml (module)
cobra.test.test_manipulation (module)
cobra.test.test_medium (module)
cobra.test.test_sampling (module)
cobra.test.test_sampling.conftest (module)
cobra.test.test_sampling.test_achr (module)
cobra.test.test_sampling.test_optgp (module)
cobra.test.test_sampling.test_sampling (module)
cobra.test.test_util (module)
cobra.test.test_util.test_array (module)
cobra.test.test_util.test_context (module)
cobra.test.test_util.test_solver (module)
cobra.test.test_util.test_util (module)
cobra.util (module)
cobra.util.array (module)
cobra.util.context (module)
cobra.util.solver (module)
cobra.util.util (module)
cobra_directory (in module cobra.test)
cobra_location (in module cobra.test)
CobraSBMLError
compare_models() (cobra.test.test_io.test_sbml.TestCobraIO class method)
(in module cobra.test.test_io.conftest)
compartment_finder (in module cobra.core.reaction)
compartment_shortlist (in module cobra.medium.annotations)
compartments (in module cobra.test.data.update_pickles)
compartments() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Model property)
(cobra.Reaction property)
config (in module cobra.core.reaction)
(in module cobra.io.sbml)
(in module cobra.test.data.update_pickles)
(in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_io.test_sbml)
Configuration (class in cobra)
(class in cobra.core)
(class in cobra.core.configuration)
configuration (in module cobra.core.model)
CONFIGURATION (in module cobra.flux_analysis.deletion)
(in module cobra.flux_analysis.variability)
constraint() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
constraint_matrices() (in module cobra.util)
(in module cobra.util.array)
constraints() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
construct_ll_test_model() (in module cobra.test.test_flux_analysis.test_loopless)
consuming_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute)
(cobra.summary.MetaboliteSummary attribute)
copy() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.core.Species method)
(cobra.core.species.Species method)
(cobra.Model method)
(cobra.Reaction method)
(cobra.Species method)
create_mat_dict() (in module cobra.io.mat)
create_mat_metabolite_id() (in module cobra.io.mat)
create_stoichiometric_matrix() (in module cobra.util)
(in module cobra.util.array)
create_test_model() (in module cobra.test)
D
data_dir (in module cobra.test)
data_directory() (in module cobra.test.conftest)
delete() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
delete_model_genes() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
demands() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
description() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
dict_list() (in module cobra.test.test_core.test_dictlist)
DictList (class in cobra)
(class in cobra.core)
(class in cobra.core.dictlist)
double_gene_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
double_reaction_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
dress_results() (cobra.core.LegacySolution method)
(cobra.core.solution.LegacySolution method)
dump() (cobra.io.yaml.MyYAML method)
E
ecoli_model (in module cobra.test.data.update_pickles)
element_re (in module cobra.core.formula)
(in module cobra.core.metabolite)
elements() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
elements_and_molecular_weights (in module cobra.core.formula)
empty_model() (in module cobra.test.conftest)
empty_once() (in module cobra.test.conftest)
equalities (in module cobra.sampling.hr_sampler)
escape_ID() (in module cobra.manipulation)
(in module cobra.manipulation.modify)
eval_gpr() (in module cobra.core.gene)
exchanges() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
excludes (in module cobra.medium.annotations)
extend() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
extend_model() (cobra.flux_analysis.gapfilling.GapFiller method)
extra_comparisons() (cobra.test.test_io.test_sbml.TestCobraIO class method)
F
f (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
F_GENE (in module cobra.io.sbml)
F_GENE_REV (in module cobra.io.sbml)
F_GROUP (in module cobra.io.sbml)
F_GROUP_REV (in module cobra.io.sbml)
F_REACTION (in module cobra.io.sbml)
F_REACTION_REV (in module cobra.io.sbml)
F_REPLACE (in module cobra.io.sbml)
F_SPECIE (in module cobra.io.sbml)
F_SPECIE_REV (in module cobra.io.sbml)
fastcc() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.fastcc)
feasibility_tol (cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
FeasibleButNotOptimal
figure1_model() (in module cobra.test.test_flux_analysis.test_fastcc)
fill() (cobra.flux_analysis.gapfilling.GapFiller method)
find_blocked_reactions() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
find_boundary_types() (in module cobra.medium)
(in module cobra.medium.boundary_types)
find_carbon_sources() (in module cobra.flux_analysis.phenotype_phase_plane)
find_essential_genes() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
find_essential_reactions() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
find_external_compartment() (in module cobra.medium)
(in module cobra.medium.boundary_types)
find_gene_knockout_reactions() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
fix_objective_as_constraint() (in module cobra.util)
(in module cobra.util.solver)
flux() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
flux_expression() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
flux_variability_analysis() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.variability)
fluxes (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
format_long_string() (in module cobra.util)
(in module cobra.util.util)
Formula (class in cobra.core.formula)
formula_weight() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
forward_variable() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
from_json() (in module cobra.io)
(in module cobra.io.json)
from_mat_struct() (in module cobra.io.mat)
from_yaml() (in module cobra.io)
(in module cobra.io.yaml)
functional() (cobra.core.Gene property)
(cobra.core.gene.Gene property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Gene property)
(cobra.Reaction property)
fva_result (in module cobra.test.data.update_pickles)
,
[1]
fva_results() (in module cobra.test.conftest)
fwd_idx (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
G
gapfill() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.gapfilling)
GapFiller (class in cobra.flux_analysis.gapfilling)
Gene (class in cobra)
(class in cobra.core)
(class in cobra.core.gene)
gene_from_dict() (in module cobra.io.dict)
gene_name_reaction_rule() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
gene_names (in module cobra.test.data.update_pickles)
gene_reaction_rule (in module cobra.test.data.update_pickles)
gene_reaction_rule() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
gene_to_dict() (in module cobra.io.dict)
generate_fva_warmup() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
genes (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
genes() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
geometric_fba() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.geometric)
geometric_fba_model() (in module cobra.test.test_flux_analysis.test_geometric)
get_associated_groups() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
get_by_any() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
get_by_id() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
get_coefficient() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
get_coefficients() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
get_compartments() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
get_compiled_gene_reaction_rules() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
get_context() (in module cobra.util)
,
[1]
(in module cobra.util.context)
get_ids() (in module cobra.test.test_io.test_io_order)
get_metabolite_compartments() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
get_primal_by_id (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
get_solution() (in module cobra.core)
(in module cobra.core.solution)
get_solver_name() (in module cobra.util)
(in module cobra.util.solver)
gpr_clean (in module cobra.core.reaction)
GPRCleaner (class in cobra.core.gene)
Group (class in cobra.core)
(class in cobra.core.group)
groups (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
H
has_id() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
has_primals (in module cobra.util)
(in module cobra.util.solver)
HistoryManager (class in cobra.util)
(class in cobra.util.context)
homogeneous (in module cobra.sampling.hr_sampler)
HRSampler (class in cobra.sampling)
(class in cobra.sampling.hr_sampler)
I
id() (cobra.core.Object property)
(cobra.core.object.Object property)
(cobra.Object property)
index() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
inequalities (in module cobra.sampling.hr_sampler)
Infeasible
insert() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
interface_to_str() (in module cobra.util)
(in module cobra.util.solver)
io_trial() (in module cobra.test.test_io.test_sbml)
IOTrial (in module cobra.test.test_io.test_sbml)
is_boundary_type() (in module cobra.medium)
(in module cobra.medium.boundary_types)
J
json_schema_v1() (in module cobra.test.test_io.test_json)
JSON_SPEC (in module cobra.io.json)
jsonschema (in module cobra.test.test_io.test_sbml)
K
keyword_re (in module cobra.core.gene)
keywords (in module cobra.core.gene)
kind() (cobra.core.Group property)
(cobra.core.group.Group property)
KIND_TYPES (cobra.core.Group attribute)
(cobra.core.group.Group attribute)
knock_out() (cobra.core.Gene method)
(cobra.core.gene.Gene method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Gene method)
(cobra.Reaction method)
KnockoutAccessor (class in cobra.flux_analysis.deletion)
L
large_model() (in module cobra.test.conftest)
large_once() (in module cobra.test.conftest)
LegacySolution (class in cobra.core)
(class in cobra.core.solution)
linear_reaction_coefficients() (in module cobra.util)
(in module cobra.util.solver)
list_attr() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
ll_test_model() (in module cobra.test.test_flux_analysis.test_loopless)
load_json_model() (in module cobra.io)
(in module cobra.io.json)
load_matlab_model() (in module cobra.io)
(in module cobra.io.mat)
load_yaml_model() (in module cobra.io)
(in module cobra.io.yaml)
logger (in module cobra.core.model)
LOGGER (in module cobra.flux_analysis.deletion)
(in module cobra.flux_analysis.geometric)
(in module cobra.flux_analysis.helpers)
(in module cobra.flux_analysis.loopless)
(in module cobra.flux_analysis.parsimonious)
(in module cobra.flux_analysis.phenotype_phase_plane)
(in module cobra.flux_analysis.variability)
(in module cobra.io.sbml)
(in module cobra.medium.boundary_types)
(in module cobra.medium.minimal_medium)
(in module cobra.sampling.hr_sampler)
logger (in module cobra.summary.metabolite_summary)
(in module cobra.summary.model_summary)
(in module cobra.summary.reaction_summary)
(in module cobra.summary.summary)
LOGGER (in module cobra.test.test_io.test_io_order)
LONG_SHORT_DIRECTION (in module cobra.io.sbml)
loopless_fva_iter() (in module cobra.flux_analysis.loopless)
loopless_solution() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.loopless)
lower_bound (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(in module cobra.test.data.update_pickles)
lower_bound() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
LOWER_BOUND_ID (in module cobra.io.sbml)
M
MAX_TRIES (in module cobra.sampling.hr_sampler)
media_compositions (in module cobra.test.data.update_pickles)
medium() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
medium_model() (in module cobra.test.conftest)
members() (cobra.core.Group property)
(cobra.core.group.Group property)
merge() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
Metabolite (class in cobra)
(class in cobra.core)
(class in cobra.core.metabolite)
metabolite_from_dict() (in module cobra.io.dict)
metabolite_to_dict() (in module cobra.io.dict)
metabolites (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
metabolites() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
(in module cobra.test.conftest)
MetaboliteSummary (class in cobra.summary)
(class in cobra.summary.metabolite_summary)
mini (in module cobra.test.data.update_pickles)
mini_model() (in module cobra.test.test_io.conftest)
minimal_medium() (in module cobra.medium)
(in module cobra.medium.minimal_medium)
minimized_reverse() (in module cobra.test.test_io.test_io_order)
minimized_shuffle() (in module cobra.test.test_io.test_io_order)
minimized_sorted() (in module cobra.test.test_io.test_io_order)
Model (class in cobra)
(class in cobra.core)
(class in cobra.core.model)
model (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
model() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.core.Species property)
(cobra.core.species.Species property)
(cobra.Reaction property)
(cobra.Species property)
(in module cobra.test.conftest)
model_from_dict() (in module cobra.io)
(in module cobra.io.dict)
model_to_dict() (in module cobra.io)
(in module cobra.io.dict)
model_to_pymatbridge() (in module cobra.io.mat)
ModelSummary (class in cobra.summary)
(class in cobra.summary.model_summary)
moma() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.moma)
MyYAML (class in cobra.io.yaml)
N
n_samples (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
name (in module cobra.test.data.update_pickles)
normalize_cutoff() (in module cobra.flux_analysis.helpers)
NOT_MASS_BALANCED_TERMS (in module cobra.manipulation.validate)
nproj (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
nullspace (in module cobra.sampling.hr_sampler)
nullspace() (in module cobra.util)
(in module cobra.util.array)
number_start_re (in module cobra.core.gene)
O
Object (class in cobra)
(class in cobra.core)
(class in cobra.core.object)
objective (in module cobra.test.data.update_pickles)
objective() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
objective_coefficient() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
objective_direction() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
objective_value (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
opposing_model() (in module cobra.test.test_flux_analysis.test_fastcc)
opt_solver() (in module cobra.test.conftest)
optgp() (in module cobra.test.test_sampling.test_optgp)
OptGPSampler (class in cobra.sampling)
(class in cobra.sampling.optgp)
OptimizationError
,
[1]
optimize() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
optimize_minimal_flux() (in module cobra.flux_analysis.parsimonious)
optlang_solvers (in module cobra.test.test_core.test_model)
(in module cobra.test.test_util.test_solver)
OPTLANG_TO_EXCEPTIONS_DICT (in module cobra.exceptions)
(in module cobra.util)
P
parse_composition() (cobra.core.formula.Formula method)
parse_gpr() (in module cobra.core.gene)
pattern_from_sbml (in module cobra.io.sbml)
pattern_notes (in module cobra.io.sbml)
pattern_to_sbml (in module cobra.io.sbml)
pfba() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.parsimonious)
pfba_fva_results() (in module cobra.test.conftest)
pop() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
prev (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
problem (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
Problem (in module cobra.sampling.hr_sampler)
problem() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
processes (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
producing_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute)
(cobra.summary.MetaboliteSummary attribute)
production_envelope() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.phenotype_phase_plane)
products() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
prune_unused_metabolites() (in module cobra.manipulation.delete)
prune_unused_reactions() (in module cobra.manipulation.delete)
pytest (in module cobra.test)
pytest_addoption() (in module cobra.test.conftest)
Q
qp_solvers (in module cobra.util)
(in module cobra.util.solver)
qp_solvers() (in module cobra.test.test_flux_analysis.conftest)
QUALIFIER_TYPES (in module cobra.io.sbml)
query() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
R
r (in module cobra.test.data.update_pickles)
raven (in module cobra.test.data.update_pickles)
raven_model() (in module cobra.test.test_io.test_mat)
reactants() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
Reaction (class in cobra)
(class in cobra.core)
(class in cobra.core.reaction)
reaction() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
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 attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
reactions() (cobra.core.Species property)
(cobra.core.species.Species property)
(cobra.Species property)
ReactionSummary (class in cobra.summary.reaction_summary)
read_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
(in module cobra.test)
reduced_cost() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reduced_costs (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
remove() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
remove_cons_vars() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
remove_cons_vars_from_problem() (in module cobra.util)
(in module cobra.util.solver)
remove_from_model() (cobra.core.Gene method)
(cobra.core.gene.Gene method)
(cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Gene method)
(cobra.Metabolite method)
(cobra.Reaction method)
remove_genes() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
remove_groups() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
remove_members() (cobra.core.Group method)
(cobra.core.group.Group method)
remove_metabolites() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
remove_reactions() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
rename_genes() (in module cobra.manipulation.modify)
repair() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
replacements (in module cobra.core.gene)
reset() (cobra.util.context.HistoryManager method)
(cobra.util.HistoryManager method)
resettable() (in module cobra.util)
(in module cobra.util.context)
retries (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
rev_idx (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
reverse() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
reverse_id() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reverse_variable() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
reversibility() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
room() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.room)
room_model() (in module cobra.test.test_flux_analysis.conftest)
room_solution() (in module cobra.test.test_flux_analysis.conftest)
S
salmonella (in module cobra.test.data.update_pickles)
salmonella() (in module cobra.test.conftest)
same_ex() (in module cobra.test.test_core.test_model)
sample() (cobra.sampling.achr.ACHRSampler method)
(cobra.sampling.ACHRSampler method)
(cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
(cobra.sampling.optgp.OptGPSampler method)
(cobra.sampling.OptGPSampler method)
(in module cobra.sampling)
(in module cobra.sampling.sampling)
save_json_model() (in module cobra.io)
(in module cobra.io.json)
save_matlab_model() (in module cobra.io)
(in module cobra.io.mat)
save_yaml_model() (in module cobra.io)
(in module cobra.io.yaml)
SBML_DOT (in module cobra.io.sbml)
SBO_DEFAULT_FLUX_BOUND (in module cobra.io.sbml)
SBO_EXCHANGE_REACTION (in module cobra.io.sbml)
SBO_FBA_FRAMEWORK (in module cobra.io.sbml)
SBO_FLUX_BOUND (in module cobra.io.sbml)
sbo_terms (in module cobra.medium)
(in module cobra.medium.annotations)
scipy (in module cobra.test.test_io.test_mat)
scipy_sparse (in module cobra.io.mat)
secretion_flux (cobra.summary.model_summary.ModelSummary attribute)
(cobra.summary.ModelSummary attribute)
seed (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
set_objective() (in module cobra.util)
(in module cobra.util.solver)
shadow_price() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
shadow_prices (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
shared_np_array() (in module cobra.sampling)
(in module cobra.sampling.hr_sampler)
SHORT_LONG_DIRECTION (in module cobra.io.sbml)
show_versions() (in module cobra)
(in module cobra.util)
(in module cobra.util.util)
single_gene_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
single_reaction_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
Singleton (class in cobra.core.singleton)
sinks() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
size() (cobra.util.context.HistoryManager method)
(cobra.util.HistoryManager method)
slim_optimize() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
small_model() (in module cobra.test.conftest)
Solution (class in cobra)
(class in cobra.core)
(class in cobra.core.solution)
solution (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
(in module cobra.test.data.update_pickles)
solved_model() (in module cobra.test.conftest)
(in module cobra.test.test_core.conftest)
solver (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
(in module cobra.test.data.update_pickles)
solver() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
(cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
solver_trials (in module cobra.test.test_core.conftest)
SolverNotFound
,
[1]
solvers (in module cobra.util)
(in module cobra.util.solver)
sort() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
Species (class in cobra)
(class in cobra.core)
(class in cobra.core.species)
stable_optlang (in module cobra.test.conftest)
(in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_model)
(in module cobra.test.test_util.test_solver)
status (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
step() (in module cobra.sampling)
(in module cobra.sampling.hr_sampler)
subtract_metabolites() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
Summary (class in cobra.summary)
(class in cobra.summary.summary)
summary() (cobra.core.Metabolite method)
(cobra.core.metabolite.Metabolite method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Metabolite method)
(cobra.Model method)
(cobra.Reaction method)
T
template() (in module cobra.test.test_io.test_io_order)
test_absolute_expression() (in module cobra.test.test_util.test_solver)
test_achr_init_benchmark() (in module cobra.test.test_sampling.test_achr)
test_achr_sample_benchmark() (in module cobra.test.test_sampling.test_achr)
test_add() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_dictlist)
test_add_boundary() (in module cobra.test.test_core.test_model)
test_add_boundary_context() (in module cobra.test.test_core.test_model)
test_add_cobra_reaction() (in module cobra.test.test_core.test_model)
test_add_existing_boundary() (in module cobra.test.test_core.test_model)
test_add_lexicographic_constraints() (in module cobra.test.test_util.test_solver)
test_add_loopless() (in module cobra.test.test_flux_analysis.test_loopless)
test_add_lp_feasibility() (in module cobra.test.test_util.test_solver)
test_add_metabolite() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_model)
test_add_metabolite_benchmark() (in module cobra.test.test_core.test_core_reaction)
test_add_metabolite_from_solved_model() (in module cobra.test.test_core.test_core_reaction)
test_add_metabolites_combine_false() (in module cobra.test.test_core.test_core_reaction)
test_add_metabolites_combine_true() (in module cobra.test.test_core.test_core_reaction)
test_add_reaction() (in module cobra.test.test_core.test_model)
test_add_reaction_context() (in module cobra.test.test_core.test_model)
test_add_reaction_from_other_model() (in module cobra.test.test_core.test_model)
test_add_reaction_orphans() (in module cobra.test.test_core.test_model)
test_add_reactions() (in module cobra.test.test_core.test_model)
test_add_reactions_duplicate() (in module cobra.test.test_core.test_model)
test_add_reactions_single_existing() (in module cobra.test.test_core.test_model)
test_add_remove() (in module cobra.test.test_util.test_solver)
test_add_remove_in_context() (in module cobra.test.test_util.test_solver)
test_add_remove_reaction_benchmark() (in module cobra.test.test_core.test_model)
test_all() (in module cobra.test)
test_all_objects_point_to_all_other_correct_objects() (in module cobra.test.test_core.test_model)
test_append() (in module cobra.test.test_core.test_dictlist)
test_assess() (in module cobra.test.test_flux_analysis.test_reaction)
test_bad_exchange() (cobra.test.test_medium.TestErrorsAndExceptions method)
test_batch_sampling() (in module cobra.test.test_sampling.test_achr)
(in module cobra.test.test_sampling.test_optgp)
test_benchmark_medium_linear() (cobra.test.test_medium.TestMinimalMedia method)
test_benchmark_medium_mip() (cobra.test.test_medium.TestMinimalMedia method)
test_boundary_conditions() (in module cobra.test.test_io.test_sbml)
test_bounds() (in module cobra.test.test_core.test_configuration)
test_bounds_setter() (in module cobra.test.test_core.test_core_reaction)
test_build_from_string() (in module cobra.test.test_core.test_core_reaction)
test_change_bounds() (in module cobra.test.test_core.test_core_reaction)
test_change_id_is_reflected_in_solver() (in module cobra.test.test_core.test_core_reaction)
test_change_objective() (in module cobra.test.test_core.test_model)
,
[1]
test_change_objective_benchmark() (in module cobra.test.test_core.test_model)
test_change_objective_through_objective_coefficient() (in module cobra.test.test_core.test_model)
test_change_solver_to_cplex_and_check_copy_works() (in module cobra.test.test_core.test_model)
test_choose_solver() (in module cobra.test.test_util.test_solver)
test_compartments() (in module cobra.test.test_core.test_model)
test_complicated_model() (in module cobra.test.test_sampling.test_sampling)
test_contains() (in module cobra.test.test_core.test_dictlist)
test_context_manager() (in module cobra.test.test_core.test_model)
test_copy() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_dictlist)
(in module cobra.test.test_core.test_model)
test_copy_benchmark() (in module cobra.test.test_core.test_model)
test_copy_benchmark_large_model() (in module cobra.test.test_core.test_model)
test_copy_preserves_existing_solution() (in module cobra.test.test_core.test_model)
test_copy_with_groups() (in module cobra.test.test_core.test_model)
test_deepcopy() (in module cobra.test.test_core.test_dictlist)
(in module cobra.test.test_core.test_model)
test_deepcopy_benchmark() (in module cobra.test.test_core.test_model)
test_default_bounds() (in module cobra.test.test_core.test_configuration)
test_default_tolerance() (in module cobra.test.test_core.test_configuration)
test_deletion_accessor() (in module cobra.test.test_flux_analysis.test_deletion)
test_demand() (cobra.test.test_medium.TestTypeDetection method)
test_dense_matrix() (in module cobra.test.test_util.test_array)
test_dir() (in module cobra.test.test_core.test_dictlist)
test_double_gene_deletion() (in module cobra.test.test_flux_analysis.test_deletion)
test_double_gene_deletion_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_double_reaction_deletion() (in module cobra.test.test_flux_analysis.test_deletion)
test_double_reaction_deletion_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_envelope_multi_reaction_objective() (in module cobra.test.test_flux_analysis.test_phenotype_phase_plane)
test_envelope_one() (in module cobra.test.test_flux_analysis.test_phenotype_phase_plane)
test_envelope_two() (in module cobra.test.test_flux_analysis.test_phenotype_phase_plane)
test_equality_constraint() (in module cobra.test.test_sampling.test_sampling)
test_escape_ids() (cobra.test.test_manipulation.TestManipulation method)
test_essential_genes() (in module cobra.test.test_flux_analysis.test_variability)
test_essential_reactions() (in module cobra.test.test_flux_analysis.test_variability)
test_exchange() (cobra.test.test_medium.TestTypeDetection method)
test_exchange_reactions() (in module cobra.test.test_core.test_model)
test_extend() (in module cobra.test.test_core.test_dictlist)
test_external_compartment() (cobra.test.test_medium.TestTypeDetection method)
test_fail_non_linear_reaction_coefficients() (in module cobra.test.test_util.test_solver)
test_fastcc_against_fva_nonblocked_rxns() (in module cobra.test.test_flux_analysis.test_fastcc)
test_fastcc_benchmark() (in module cobra.test.test_flux_analysis.test_fastcc)
test_fdp_production_with_fva() (in module test_metabolite_summary)
test_figure1() (in module cobra.test.test_flux_analysis.test_fastcc)
test_filehandle() (in module cobra.test.test_io.test_sbml)
test_find_blocked_reactions() (in module cobra.test.test_flux_analysis.test_variability)
test_find_blocked_reactions_solver_none() (in module cobra.test.test_flux_analysis.test_variability)
test_fix_objective_as_constraint() (in module cobra.test.test_util.test_solver)
test_fix_objective_as_constraint_minimize() (in module cobra.test.test_util.test_solver)
test_fixed_seed() (in module cobra.test.test_sampling.test_sampling)
test_flux_variability() (in module cobra.test.test_flux_analysis.test_variability)
test_flux_variability_benchmark() (in module cobra.test.test_flux_analysis.test_variability)
test_flux_variability_loopless() (in module cobra.test.test_flux_analysis.test_variability)
test_flux_variability_loopless_benchmark() (in module cobra.test.test_flux_analysis.test_variability)
test_formula_element_setting() (in module cobra.test.test_core.test_metabolite)
test_from_sbml_string() (in module cobra.test.test_io.test_sbml)
test_fva_data_frame() (in module cobra.test.test_flux_analysis.test_variability)
test_fva_infeasible() (in module cobra.test.test_flux_analysis.test_variability)
test_fva_minimization() (in module cobra.test.test_flux_analysis.test_variability)
test_gapfilling() (in module cobra.test.test_flux_analysis.test_gapfilling)
test_gene_knock_out() (in module cobra.test.test_core.test_core_reaction)
test_gene_knockout_computation() (cobra.test.test_manipulation.TestManipulation method)
test_geometric_fba() (in module cobra.test.test_flux_analysis.test_geometric)
test_geometric_fba_benchmark() (in module cobra.test.test_flux_analysis.test_geometric)
test_get_by_any() (in module cobra.test.test_core.test_dictlist)
test_get_context() (in module cobra.test.test_util.test_context)
test_get_objective_direction() (in module cobra.test.test_core.test_model)
test_gpr() (in module cobra.test.test_core.test_core_reaction)
test_gpr_modification() (in module cobra.test.test_core.test_core_reaction)
test_gprs() (in module cobra.test.test_io.test_sbml)
test_group_add_elements() (in module cobra.test.test_core.test_group)
test_group_kind() (in module cobra.test.test_core.test_group)
test_group_loss_of_elements() (in module cobra.test.test_core.test_model)
test_group_members_add_to_model() (in module cobra.test.test_core.test_model)
test_group_model_reaction_association() (in module cobra.test.test_core.test_model)
test_groups() (in module cobra.test.test_io.test_sbml)
test_history_manager() (in module cobra.test.test_util.test_context)
test_iadd() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_dictlist)
test_identifiers_annotation() (in module cobra.test.test_io.test_sbml)
test_independent() (in module cobra.test.test_core.test_dictlist)
test_index() (in module cobra.test.test_core.test_dictlist)
test_inequality_constraint() (in module cobra.test.test_sampling.test_sampling)
test_infinity_bounds() (in module cobra.test.test_io.test_sbml)
test_inhomogeneous_sanity() (in module cobra.test.test_sampling.test_sampling)
test_init_copy() (in module cobra.test.test_core.test_dictlist)
test_insert() (in module cobra.test.test_core.test_dictlist)
test_interface_str() (in module cobra.test.test_util.test_solver)
test_invalid_objective_raises() (in module cobra.test.test_core.test_model)
test_invalid_solver_change_raises() (in module cobra.test.test_core.test_model)
test_io_order() (in module cobra.test.test_io.test_io_order)
test_irrev_reaction_set_negative_lb() (in module cobra.test.test_core.test_core_reaction)
test_isub() (in module cobra.test.test_core.test_dictlist)
test_knockout() (in module cobra.test.test_core.test_core_reaction)
test_linear_moma_sanity() (in module cobra.test.test_flux_analysis.test_moma)
test_linear_reaction_coefficients() (in module cobra.test.test_util.test_solver)
test_linear_room_sanity() (in module cobra.test.test_flux_analysis.test_room)
test_load_json_model() (in module cobra.test.test_io.test_json)
test_load_json_model_invalid() (in module cobra.test.test_io.test_annotation_format)
test_load_json_model_valid() (in module cobra.test.test_io.test_annotation_format)
test_load_matlab_model() (in module cobra.test.test_io.test_mat)
test_load_yaml_model() (in module cobra.test.test_io.test_yaml)
test_loopless_benchmark_after() (in module cobra.test.test_flux_analysis.test_loopless)
test_loopless_benchmark_before() (in module cobra.test.test_flux_analysis.test_loopless)
test_loopless_pfba_fva() (in module cobra.test.test_flux_analysis.test_variability)
test_loopless_solution() (in module cobra.test.test_flux_analysis.test_loopless)
test_loopless_solution_fluxes() (in module cobra.test.test_flux_analysis.test_loopless)
test_make_irreversible() (in module cobra.test.test_core.test_core_reaction)
test_make_irreversible_irreversible_to_the_other_side() (in module cobra.test.test_core.test_core_reaction)
test_make_lhs_irreversible_reversible() (in module cobra.test.test_core.test_core_reaction)
test_make_reversible() (in module cobra.test.test_core.test_core_reaction)
test_mass_balance() (in module cobra.test.test_core.test_core_reaction)
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() (in module cobra.test.test_core.test_model)
test_metabolite_formula() (in module cobra.test.test_core.test_metabolite)
test_metabolite_summary (module)
test_metabolite_summary_flux_in_context() (in module test_metabolite_summary)
test_metabolite_summary_interface() (in module test_metabolite_summary)
test_metabolite_summary_to_frame() (in module test_metabolite_summary)
test_metabolite_summary_to_html() (in module test_metabolite_summary)
test_metabolite_summary_to_string() (in module test_metabolite_summary)
test_missing_flux_bounds1() (in module cobra.test.test_io.test_sbml)
test_missing_flux_bounds2() (in module cobra.test.test_io.test_sbml)
test_model_from_other_model() (in module cobra.test.test_core.test_model)
test_model_history() (in module cobra.test.test_io.test_sbml)
test_model_less_reaction() (in module cobra.test.test_core.test_core_reaction)
test_model_medium() (cobra.test.test_medium.TestModelMedium method)
test_model_remove_reaction() (in module cobra.test.test_core.test_model)
test_model_summary (module)
test_model_summary_flux() (in module test_model_summary)
test_model_summary_flux_in_context() (in module test_model_summary)
test_model_summary_fva() (in module test_model_summary)
test_model_summary_interface() (in module test_model_summary)
test_model_summary_to_frame() (in module test_model_summary)
test_model_summary_to_frame_previous_solution() (in module test_model_summary)
test_model_summary_to_html() (in module test_model_summary)
test_model_summary_to_string() (in module test_model_summary)
test_moma_sanity() (in module cobra.test.test_flux_analysis.test_moma)
test_mul() (in module cobra.test.test_core.test_core_reaction)
test_multi_external() (cobra.test.test_medium.TestTypeDetection method)
test_multi_optgp() (in module cobra.test.test_sampling.test_sampling)
test_multi_variable_envelope() (in module cobra.test.test_flux_analysis.test_phenotype_phase_plane)
test_no_boundary_reactions() (cobra.test.test_medium.TestErrorsAndExceptions method)
test_no_change_for_same_solver() (in module cobra.test.test_core.test_model)
test_no_names_or_boundary_reactions() (cobra.test.test_medium.TestErrorsAndExceptions method)
test_notes() (in module cobra.test.test_io.test_notes)
test_objective() (in module cobra.test.test_core.test_model)
test_objective_coefficient_reflects_changed_objective() (in module cobra.test.test_core.test_model)
test_objects_point_to_correct_other_after_copy() (in module cobra.test.test_core.test_model)
test_one_left_to_right_reaction_set_positive_ub() (in module cobra.test.test_core.test_core_reaction)
test_open_exchanges() (cobra.test.test_medium.TestMinimalMedia method)
test_opposing() (in module cobra.test.test_flux_analysis.test_fastcc)
test_optgp_init_benchmark() (in module cobra.test.test_sampling.test_optgp)
test_optgp_sample_benchmark() (in module cobra.test.test_sampling.test_optgp)
test_optimize() (in module cobra.test.test_core.test_model)
test_parallel_flux_variability() (in module cobra.test.test_flux_analysis.test_variability)
test_pfba() (in module cobra.test.test_flux_analysis.test_parsimonious)
test_pfba_benchmark() (in module cobra.test.test_flux_analysis.test_parsimonious)
test_pfba_flux_variability() (in module cobra.test.test_flux_analysis.test_variability)
test_pickle() (in module cobra.test.test_core.test_dictlist)
test_problem_properties() (in module cobra.test.test_core.test_model)
test_prune_unused_mets_functionality() (cobra.test.test_manipulation.TestManipulation method)
test_prune_unused_mets_output_type() (cobra.test.test_manipulation.TestManipulation method)
test_prune_unused_rxns_functionality() (cobra.test.test_manipulation.TestManipulation method)
test_prune_unused_rxns_output_type() (cobra.test.test_manipulation.TestManipulation method)
test_q8_consuming_summary() (in module test_metabolite_summary)
test_q8_producing_summary() (in module test_metabolite_summary)
test_query() (in module cobra.test.test_core.test_dictlist)
test_radd() (in module cobra.test.test_core.test_core_reaction)
test_reaction_bounds_json() (in module cobra.test.test_io.test_json)
test_reaction_delete() (in module cobra.test.test_core.test_model)
test_reaction_imul() (in module cobra.test.test_core.test_core_reaction)
test_reaction_remove() (in module cobra.test.test_core.test_model)
test_reaction_summary (module)
test_reaction_summary_flux() (in module test_reaction_summary)
test_reaction_summary_flux_fva() (in module test_reaction_summary)
test_reaction_summary_flux_in_context() (in module test_reaction_summary)
test_reaction_summary_interface() (in module test_reaction_summary)
test_reaction_summary_to_frame() (in module test_reaction_summary)
test_reaction_summary_to_html() (in module test_reaction_summary)
test_reaction_summary_to_string() (in module test_reaction_summary)
test_reaction_without_model() (in module cobra.test.test_core.test_core_reaction)
test_read_1() (cobra.test.test_io.test_sbml.TestCobraIO method)
test_read_2() (cobra.test.test_io.test_sbml.TestCobraIO method)
test_read_pickle() (in module cobra.test.test_io.test_pickle)
test_read_sbml_annotations() (in module cobra.test.test_io.test_annotation)
test_read_write_sbml_annotations() (in module cobra.test.test_io.test_annotation)
test_removal() (in module cobra.test.test_core.test_dictlist)
test_removal_from_model_retains_bounds() (in module cobra.test.test_core.test_core_reaction)
test_remove_from_model() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_metabolite)
test_remove_gene() (in module cobra.test.test_core.test_model)
test_remove_genes() (cobra.test.test_manipulation.TestManipulation method)
test_remove_metabolite_destructive() (in module cobra.test.test_core.test_model)
test_remove_metabolite_subtractive() (in module cobra.test.test_core.test_model)
test_remove_reactions() (in module cobra.test.test_core.test_model)
test_rename_gene() (cobra.test.test_manipulation.TestManipulation method)
test_repr_html_() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_gene)
(in module cobra.test.test_core.test_metabolite)
(in module cobra.test.test_core.test_model)
test_reproject() (in module cobra.test.test_sampling.test_optgp)
test_resettable() (in module cobra.test.test_util.test_context)
test_room_sanity() (in module cobra.test.test_flux_analysis.test_room)
test_sampling() (in module cobra.test.test_sampling.test_achr)
(in module cobra.test.test_sampling.test_optgp)
test_save_json_model() (in module cobra.test.test_io.test_json)
test_save_matlab_model() (in module cobra.test.test_io.test_mat)
test_save_yaml_model() (in module cobra.test.test_io.test_yaml)
test_sbo_annotation() (cobra.test.test_manipulation.TestManipulation method)
test_sbo_terms() (cobra.test.test_medium.TestTypeDetection method)
test_set() (in module cobra.test.test_core.test_dictlist)
test_set_bounds_scenario_1() (in module cobra.test.test_core.test_core_reaction)
test_set_bounds_scenario_2() (in module cobra.test.test_core.test_core_reaction)
test_set_bounds_scenario_3() (in module cobra.test.test_core.test_core_reaction)
test_set_bounds_scenario_4() (in module cobra.test.test_core.test_core_reaction)
test_set_id() (in module cobra.test.test_core.test_metabolite)
test_set_lb_higher_than_ub_sets_ub_to_new_lb() (in module cobra.test.test_core.test_core_reaction)
test_set_objective_direction() (in module cobra.test.test_core.test_model)
test_set_reaction_objective() (in module cobra.test.test_core.test_model)
test_set_reaction_objective_str() (in module cobra.test.test_core.test_model)
test_set_ub_lower_than_lb_sets_lb_to_new_ub() (in module cobra.test.test_core.test_core_reaction)
test_set_upper_before_lower_bound_to_0() (in module cobra.test.test_core.test_core_reaction)
test_show_versions() (in module cobra.test.test_util.test_util)
test_single_achr() (in module cobra.test.test_sampling.test_sampling)
test_single_gene_deletion_fba() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_fba_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_linear_moma() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_linear_moma_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_linear_room_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_moma() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_moma_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_moma_reference() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_gene_deletion_room_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_optgp() (in module cobra.test.test_sampling.test_sampling)
test_single_point_space() (in module cobra.test.test_sampling.test_sampling)
test_single_reaction_deletion() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_reaction_deletion_benchmark() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_reaction_deletion_linear_room() (in module cobra.test.test_flux_analysis.test_deletion)
test_single_reaction_deletion_room() (in module cobra.test.test_flux_analysis.test_deletion)
test_sink() (cobra.test.test_medium.TestTypeDetection method)
test_slice() (in module cobra.test.test_core.test_dictlist)
test_slim_optimize() (in module cobra.test.test_core.test_model)
test_smbl_with_notes() (in module cobra.test.test_io.test_sbml)
test_solution_contains_only_reaction_specific_values() (in module cobra.test.test_core.test_solution)
test_solution_data_frame() (in module cobra.test.test_core.test_model)
test_solver() (in module cobra.test.test_core.test_configuration)
test_solver_change() (in module cobra.test.test_core.test_model)
test_solver_list() (in module cobra.test.test_util.test_solver)
test_solver_name() (in module cobra.test.test_util.test_solver)
test_sort_and_reverse() (in module cobra.test.test_core.test_dictlist)
test_sparse_matrix() (in module cobra.test.test_util.test_array)
test_str() (in module cobra.test.test_core.test_core_reaction)
test_str_from_model() (in module cobra.test.test_core.test_core_reaction)
test_sub() (in module cobra.test.test_core.test_core_reaction)
(in module cobra.test.test_core.test_dictlist)
test_subtract_metabolite() (in module cobra.test.test_core.test_core_reaction)
test_subtract_metabolite_benchmark() (in module cobra.test.test_core.test_core_reaction)
test_time_limit() (in module cobra.test.test_util.test_solver)
test_tolerance_assignment() (in module cobra.test.test_core.test_configuration)
test_toy_model_tolerance_with_different_default() (in module cobra.test.test_core.test_configuration)
test_transfer_objective() (in module cobra.test.test_core.test_model)
test_twist_irrev_right_to_left_reaction_to_left_to_right() (in module cobra.test.test_core.test_core_reaction)
test_union() (in module cobra.test.test_core.test_dictlist)
test_validate() (in module cobra.test.test_io.test_sbml)
,
[1]
test_validate_formula_compartment() (cobra.test.test_manipulation.TestManipulation method)
test_validate_json() (in module cobra.test.test_io.test_json)
test_validate_mass_balance() (cobra.test.test_manipulation.TestManipulation method)
test_validate_wrong_sample() (in module cobra.test.test_sampling.test_achr)
test_validation_warnings() (in module cobra.test.test_io.test_sbml)
test_variables_samples() (in module cobra.test.test_sampling.test_achr)
(in module cobra.test.test_sampling.test_optgp)
test_weird_left_to_right_reaction_issue() (in module cobra.test.test_core.test_core_reaction)
test_write_1() (cobra.test.test_io.test_sbml.TestCobraIO method)
test_write_2() (cobra.test.test_io.test_sbml.TestCobraIO method)
test_write_pickle() (in module cobra.test.test_io.test_pickle)
test_wrong_method() (in module cobra.test.test_sampling.test_sampling)
TestCobraIO (class in cobra.test.test_io.test_sbml)
TestErrorsAndExceptions (class in cobra.test.test_medium)
TestManipulation (class in cobra.test.test_manipulation)
TestMinimalMedia (class in cobra.test.test_medium)
TestModelMedium (class in cobra.test.test_medium)
TestTypeDetection (class in cobra.test.test_medium)
textbook (in module cobra.test.data.update_pickles)
tg (in module cobra.test.data.update_pickles)
thinning (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
tiny_toy_model() (in module cobra.test.conftest)
tmp_path() (in module cobra.test.test_io.test_io_order)
to_frame() (cobra.core.Solution method)
(cobra.core.solution.Solution method)
(cobra.Solution method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_html() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_json() (in module cobra.io)
(in module cobra.io.json)
to_string() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_yaml() (in module cobra.io)
(in module cobra.io.yaml)
tolerance (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
tolerance() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
(cobra.summary.Summary property)
(cobra.summary.summary.Summary property)
total_components_flux() (in module cobra.flux_analysis.phenotype_phase_plane)
total_yield() (in module cobra.flux_analysis.phenotype_phase_plane)
trial_names (in module cobra.test.test_io.test_sbml)
trials (in module cobra.test.test_io.test_sbml)
U
Unbounded
UndefinedSolution
undelete_model_genes() (in module cobra.manipulation)
(in module cobra.manipulation.delete)
union() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
Unit (in module cobra.io.sbml)
UNITS_FLUX (in module cobra.io.sbml)
update_costs() (cobra.flux_analysis.gapfilling.GapFiller method)
update_variable_bounds() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
upper_bound (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(in module cobra.test.data.update_pickles)
,
[1]
upper_bound() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
UPPER_BOUND_ID (in module cobra.io.sbml)
uppercase_AND (in module cobra.core.reaction)
uppercase_OR (in module cobra.core.reaction)
uptake_flux (cobra.summary.model_summary.ModelSummary attribute)
(cobra.summary.ModelSummary attribute)
URL_IDENTIFIERS_PATTERN (in module cobra.io.sbml)
URL_IDENTIFIERS_PREFIX (in module cobra.io.sbml)
V
validate() (cobra.flux_analysis.gapfilling.GapFiller method)
(cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
validate_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
variable_bounds (in module cobra.sampling.hr_sampler)
variables() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
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.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
weight() (cobra.core.formula.Formula property)
write_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
X
x (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
x() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
x_dict (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
Y
y (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
y() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Metabolite property)
(cobra.Reaction property)
y_dict (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
yaml (in module cobra.io.yaml)
YAML_SPEC (in module cobra.io.yaml)
Z
ZERO_BOUND_ID (in module cobra.io.sbml)
Read the Docs
v: 0.19.0
Versions
latest
0.25.0
0.24.0
0.23.0
0.22.1
0.21.0
0.20.0
0.19.0
0.18.1
0.17.1
0.16.0
0.15.4
0.14.1
0.14.0
0.13.4
0.13.3
0.13.2
0.13.1
0.13.0
0.12.1
0.12.0
0.11.3
0.11.2
0.11.1
0.11.0
0.10.1
0.10.0
0.9.1
0.9.0
0.8.2
0.8.1
0.8.0
0.7.0
0.6.2
0.6.1
0.6.0
0.5.11
0.5.10
0.5.9
0.5.8
0.5.7
0.5.6
0.5.4
0.5.3
0.5.2
0.4.1
0.4.0
0.3.2
devel
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.