cobra
0.18.1
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
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Index
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Index
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B
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C
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O
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P
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Q
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T
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Y
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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)
__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.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.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.core.Summary method)
(cobra.core.summary.Summary method)
(cobra.core.summary.summary.Summary method)
(cobra.Object method)
(cobra.Reaction 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)
_cobra_path (in module cobra)
_create_bound() (in module cobra.io.sbml)
_create_parameter() (in module cobra.io.sbml)
_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.core.MetaboliteSummary method)
(cobra.core.Summary method)
(cobra.core.summary.metabolite_summary.MetaboliteSummary method)
(cobra.core.summary.MetaboliteSummary method)
(cobra.core.summary.model_summary.ModelSummary method)
(cobra.core.summary.ModelSummary method)
(cobra.core.summary.Summary method)
(cobra.core.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)
_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)
_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)
_process_flux_dataframe() (cobra.core.Summary method)
(cobra.core.summary.Summary method)
(cobra.core.summary.summary.Summary 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.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.core.Summary method)
(cobra.core.summary.Summary method)
(cobra.core.summary.summary.Summary method)
(cobra.Gene method)
(cobra.Metabolite method)
(cobra.Model method)
(cobra.Reaction method)
(cobra.Solution 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_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)
_to_table() (cobra.core.MetaboliteSummary method)
(cobra.core.Summary method)
(cobra.core.summary.metabolite_summary.MetaboliteSummary method)
(cobra.core.summary.MetaboliteSummary method)
(cobra.core.summary.model_summary.ModelSummary method)
(cobra.core.summary.ModelSummary method)
(cobra.core.summary.Summary method)
(cobra.core.summary.summary.Summary 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)
_warn_format() (in module cobra)
_warning_base (in module cobra)
A
achr() (in module 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)
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 (in module cobra.sampling.hr_sampler)
bounds() (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
captured_output() (in module cobra.test.test_core.test_summary)
center (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
check_in_line() (in module cobra.test.test_core.test_summary)
check_line() (in module cobra.test.test_core.test_summary)
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 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.core.summary (module)
cobra.core.summary.metabolite_summary (module)
cobra.core.summary.model_summary (module)
cobra.core.summary.summary (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.test (module)
cobra.test.conftest (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_core.test_summary (module)
cobra.test.test_core.test_summary.test_metabolite_summary (module)
cobra.test.test_core.test_summary.test_model_summary (module)
cobra.test.test_core.test_summary.test_reaction_summary (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.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 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.test_core.test_core_reaction)
(in module cobra.test.test_io.test_sbml)
(in module update_pickles)
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)
conftest (module)
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 test_loopless)
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 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 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)
float_format (cobra.core.Summary attribute)
(cobra.core.summary.Summary attribute)
(cobra.core.summary.summary.Summary attribute)
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)
formatwarning (in module cobra)
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 (cobra.core.Summary attribute)
(cobra.core.summary.Summary attribute)
(cobra.core.summary.summary.Summary attribute)
fva_result (in module 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 update_pickles)
gene_reaction_rule (in module 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 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 (in module cobra.io.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)
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 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)
(in module cobra.core.summary.model_summary)
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)
(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 (in module 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 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 (cobra.core.MetaboliteSummary attribute)
(cobra.core.summary.metabolite_summary.MetaboliteSummary attribute)
(cobra.core.summary.MetaboliteSummary attribute)
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.core)
(class in cobra.core.summary)
(class in cobra.core.summary.metabolite_summary)
mini (in module 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.core.Summary attribute)
(cobra.core.summary.Summary attribute)
(cobra.core.summary.summary.Summary attribute)
(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.core.summary)
(class in cobra.core.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 update_pickles)
names (cobra.core.Summary attribute)
(cobra.core.summary.Summary attribute)
(cobra.core.summary.summary.Summary attribute)
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 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 test_fastcc)
opt_solver() (in module cobra.test.conftest)
optgp() (in module 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 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)
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)
QUALIFIER_TYPES (in module cobra.io.sbml)
query() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
R
r (in module update_pickles)
raven (in module 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)
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)
S
salmonella (in module 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)
(in module test_array)
scipy_sparse (in module cobra.io.mat)
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)
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.core.Summary attribute)
(cobra.core.summary.Summary attribute)
(cobra.core.summary.summary.Summary attribute)
(cobra.Model attribute)
(in module update_pickles)
solved_model() (in module cobra.test.conftest)
(in module cobra.test.test_core.conftest)
solver (cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
(in module update_pickles)
solver() (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 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.core)
(class in cobra.core.summary)
(class in cobra.core.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 test_solver)
test_achr (module)
test_achr_init_benchmark() (in module test_achr)
test_achr_sample_benchmark() (in module 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 test_solver)
test_add_loopless() (in module test_loopless)
test_add_lp_feasibility() (in module 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 test_solver)
test_add_remove_in_context() (in module 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_array (module)
test_assess() (in module test_reaction)
test_bad_exchange() (cobra.test.test_medium.TestErrorsAndExceptions method)
test_batch_sampling() (in module test_achr)
(in module 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 test_solver)
test_compartments() (in module cobra.test.test_core.test_model)
test_complicated_model() (in module 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 (module)
test_demand() (cobra.test.test_medium.TestTypeDetection method)
test_dense_matrix() (in module test_array)
test_dir() (in module cobra.test.test_core.test_dictlist)
test_double_gene_deletion() (in module test_deletion)
test_double_gene_deletion_benchmark() (in module test_deletion)
test_double_reaction_deletion() (in module test_deletion)
test_double_reaction_deletion_benchmark() (in module test_deletion)
test_envelope_multi_reaction_objective() (in module test_phenotype_phase_plane)
test_envelope_one() (in module test_phenotype_phase_plane)
test_envelope_two() (in module test_phenotype_phase_plane)
test_equality_constraint() (in module test_sampling)
test_escape_ids() (cobra.test.test_manipulation.TestManipulation method)
test_essential_genes() (in module test_variability)
test_essential_reactions() (in module 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 test_solver)
test_fastcc (module)
test_fastcc_against_fva_nonblocked_rxns() (in module test_fastcc)
test_fastcc_benchmark() (in module test_fastcc)
test_figure1() (in module test_fastcc)
test_filehandle() (in module cobra.test.test_io.test_sbml)
test_find_blocked_reactions() (in module test_variability)
test_find_blocked_reactions_solver_none() (in module test_variability)
test_fix_objective_as_constraint() (in module test_solver)
test_fix_objective_as_constraint_minimize() (in module test_solver)
test_fixed_seed() (in module test_sampling)
test_flux_variability() (in module test_variability)
test_flux_variability_benchmark() (in module test_variability)
test_flux_variability_loopless() (in module test_variability)
test_flux_variability_loopless_benchmark() (in module 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 test_variability)
test_fva_infeasible() (in module test_variability)
test_fva_minimization() (in module test_variability)
test_gapfilling (module)
test_gapfilling() (in module 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 (module)
test_geometric_fba() (in module test_geometric)
test_geometric_fba_benchmark() (in module test_geometric)
test_get_by_any() (in module cobra.test.test_core.test_dictlist)
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_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 test_sampling)
test_infinity_bounds() (in module cobra.test.test_io.test_sbml)
test_inhomogeneous_sanity() (in module 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 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 test_moma)
test_linear_reaction_coefficients() (in module test_solver)
test_linear_room_sanity() (in module 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 (module)
test_loopless_benchmark_after() (in module test_loopless)
test_loopless_benchmark_before() (in module test_loopless)
test_loopless_pfba_fva() (in module test_variability)
test_loopless_solution() (in module test_loopless)
test_loopless_solution_fluxes() (in module 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_to_frame() (in module cobra.test.test_core.test_summary.test_metabolite_summary)
test_metabolite_summary_to_frame_previous_solution() (in module cobra.test.test_core.test_summary.test_metabolite_summary)
test_metabolite_summary_to_frame_with_fva() (in module cobra.test.test_core.test_summary.test_metabolite_summary)
test_metabolite_summary_to_table() (in module cobra.test.test_core.test_summary.test_metabolite_summary)
test_metabolite_summary_to_table_previous_solution() (in module cobra.test.test_core.test_summary.test_metabolite_summary)
test_metabolite_summary_to_table_with_fva() (in module cobra.test.test_core.test_summary.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_to_frame() (in module cobra.test.test_core.test_summary.test_model_summary)
test_model_summary_to_frame_previous_solution() (in module cobra.test.test_core.test_summary.test_model_summary)
test_model_summary_to_frame_with_fva() (in module cobra.test.test_core.test_summary.test_model_summary)
test_model_summary_to_table() (in module cobra.test.test_core.test_summary.test_model_summary)
test_model_summary_to_table_previous_solution() (in module cobra.test.test_core.test_summary.test_model_summary)
test_model_summary_to_table_with_fva() (in module cobra.test.test_core.test_summary.test_model_summary)
test_moma (module)
test_moma_sanity() (in module 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 test_sampling)
test_multi_variable_envelope() (in module 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 test_fastcc)
test_optgp (module)
test_optgp_init_benchmark() (in module test_optgp)
test_optgp_sample_benchmark() (in module test_optgp)
test_optimize() (in module cobra.test.test_core.test_model)
test_parallel_flux_variability() (in module test_variability)
test_parsimonious (module)
test_pfba() (in module test_parsimonious)
test_pfba_benchmark() (in module test_parsimonious)
test_pfba_flux_variability() (in module test_variability)
test_phenotype_phase_plane (module)
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_query() (in module cobra.test.test_core.test_dictlist)
test_radd() (in module cobra.test.test_core.test_core_reaction)
test_reaction (module)
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_to_frame() (in module cobra.test.test_core.test_summary.test_reaction_summary)
test_reaction_summary_to_table() (in module cobra.test.test_core.test_summary.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 test_optgp)
test_room (module)
test_room_sanity() (in module test_room)
test_sampling (module)
test_sampling() (in module test_achr)
(in module 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 test_util)
test_single_achr() (in module test_sampling)
test_single_gene_deletion_fba() (in module test_deletion)
test_single_gene_deletion_fba_benchmark() (in module test_deletion)
test_single_gene_deletion_linear_moma() (in module test_deletion)
test_single_gene_deletion_linear_moma_benchmark() (in module test_deletion)
test_single_gene_deletion_linear_room_benchmark() (in module test_deletion)
test_single_gene_deletion_moma() (in module test_deletion)
test_single_gene_deletion_moma_benchmark() (in module test_deletion)
test_single_gene_deletion_moma_reference() (in module test_deletion)
test_single_gene_deletion_room_benchmark() (in module test_deletion)
test_single_optgp() (in module test_sampling)
test_single_point_space() (in module test_sampling)
test_single_reaction_deletion() (in module test_deletion)
test_single_reaction_deletion_benchmark() (in module test_deletion)
test_single_reaction_deletion_linear_room() (in module test_deletion)
test_single_reaction_deletion_room() (in module 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 (module)
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 test_solver)
test_solver_name() (in module test_solver)
test_sort_and_reverse() (in module cobra.test.test_core.test_dictlist)
test_sparse_matrix() (in module 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 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_util (module)
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 test_achr)
test_validation_warnings() (in module cobra.test.test_io.test_sbml)
test_variability (module)
test_variables_samples() (in module test_achr)
(in module 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 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 update_pickles)
tg (in module 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)
threshold (cobra.core.Summary attribute)
(cobra.core.summary.Summary attribute)
(cobra.core.summary.summary.Summary attribute)
tiny_toy_model() (in module cobra.test.conftest)
tmp_path() (in module cobra.test.test_io.test_io_order)
to_frame() (cobra.core.MetaboliteSummary method)
(cobra.core.Solution method)
(cobra.core.solution.Solution method)
(cobra.core.Summary method)
,
[1]
(cobra.core.summary.metabolite_summary.MetaboliteSummary method)
(cobra.core.summary.MetaboliteSummary method)
(cobra.core.summary.model_summary.ModelSummary method)
(cobra.core.summary.ModelSummary method)
(cobra.core.summary.Summary method)
,
[1]
(cobra.core.summary.summary.Summary method)
,
[1]
(cobra.Solution method)
to_json() (in module cobra.io)
(in module cobra.io.json)
to_yaml() (in module cobra.io)
(in module cobra.io.yaml)
tolerance() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model 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_pickles (module)
update_variable_bounds() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
upper_bound (in module 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)
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)
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