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.Reaction method) (cobra.core.reaction.Reaction method) (cobra.DictList 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.gene.GPR method) (cobra.core.GPR 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) (cobra.util.process_pool.ProcessPool method) (cobra.util.ProcessPool method) __eq__() (cobra.core.gene.GPR method) (cobra.core.GPR method) __exit__() (cobra.core.Model method) (cobra.core.model.Model method) (cobra.Model method) (cobra.util.process_pool.ProcessPool method) (cobra.util.ProcessPool method) __getattr__() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.DictList method) (cobra.util.process_pool.ProcessPool method) (cobra.util.ProcessPool method) __getitem__() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.core.Solution 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.Reaction method) (cobra.core.reaction.Reaction method) (cobra.core.Species method) (cobra.core.species.Species method) (cobra.DictList method) (cobra.Model method) (cobra.Object method) (cobra.Reaction 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.Reaction method) (cobra.core.reaction.Reaction method) (cobra.DictList 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.gene.GPR method) (cobra.core.GPR method) (cobra.core.Object method) (cobra.core.object.Object method) (cobra.core.Solution 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.gene.GPR method) (cobra.core.GPR method) (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) _add_envelope() (in module cobra.flux_analysis.phenotype_phase_plane) _add_lp7_vars() (in module cobra.flux_analysis.fastcc) _annotation (cobra.core.Object attribute) (cobra.core.object.Object attribute) (cobra.Object attribute) _any_set() (in module cobra.flux_analysis.fastcc) _as_medium() (in module cobra.medium.minimal_medium) _associate_gene() (cobra.core.Reaction method) (cobra.core.reaction.Reaction method) (cobra.Reaction method) _ast2str() (cobra.core.gene.GPR method) (cobra.core.GPR method) _bound (cobra.core.Metabolite attribute) (cobra.core.metabolite.Metabolite attribute) (cobra.Metabolite attribute) _boundary (cobra.summary.model_summary.ModelSummary attribute) (cobra.summary.ModelSummary attribute) _boundary_metabolites (cobra.summary.model_summary.ModelSummary attribute) (cobra.summary.ModelSummary attribute) _bounds_dist() (cobra.sampling.hr_sampler.HRSampler method) (cobra.sampling.HRSampler method) _bracket_re (in module cobra.io.mat) _cache_directory (cobra.Configuration attribute) (cobra.core.Configuration attribute) (cobra.core.configuration.Configuration attribute) _cell() (in module cobra.io.mat) _cell_to_float_list() (in module cobra.io.mat) _cell_to_str_list() (in module cobra.io.mat) _chebi_re (in module cobra.io.mat) _check() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.DictList method) (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) _clean_up() (cobra.util.process_pool.ProcessPool method) (cobra.util.ProcessPool method) _clip() (in module cobra.io.sbml) _create_bound() (in module cobra.io.sbml) _create_fast_snp_problem() (in module cobra.flux_analysis.fast_snp) _create_find_cyclic_reactions_problem() (in module cobra.flux_analysis.find_cyclic_reactions) _create_parameter() (in module cobra.io.sbml) _dict (cobra.core.DictList attribute) (cobra.core.dictlist.DictList attribute) (cobra.DictList attribute) _display_flux() (cobra.summary.metabolite_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) _double_punctuation_re (in module cobra.io.mat) _ec_re (in module cobra.io.mat) _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) _eval_gpr() (cobra.core.gene.GPR method) (cobra.core.GPR method) _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) _fetch_model() (in module cobra.io.web.load) _filename (cobra.util.process_pool.ProcessPool attribute) (cobra.util.ProcessPool attribute) _find_carbon_sources() (in module cobra.flux_analysis.phenotype_phase_plane) _find_sparse_mode() (in module cobra.flux_analysis.fastcc) _fix_type() (in module cobra.io.dict) _flip_coefficients() (in module cobra.flux_analysis.fastcc) _flux (cobra.summary.Summary attribute) (cobra.summary.summary.Summary attribute) _forward_arrow_finder (in module cobra.core.reaction) _functional (cobra.core.Gene attribute) (cobra.core.gene.Gene attribute) (cobra.Gene attribute) _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) _gene_to_dict() (in module cobra.io.dict) _GeneEscaper (class in cobra.manipulation.modify) _generate() (cobra.summary.metabolite_summary.MetaboliteSummary method) (cobra.summary.model_summary.ModelSummary method) (cobra.summary.ModelSummary method) (cobra.summary.reaction_summary.ReactionSummary method) (cobra.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) _genes (cobra.core.gene.GPR attribute) (cobra.core.GPR attribute) (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.Reaction attribute) _get_condition_vector() (in module cobra.flux_analysis.fast_snp) _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) _gpr (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.Reaction attribute) _history (cobra.util.context.HistoryManager attribute) (cobra.util.HistoryManager attribute) _html_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method) (cobra.summary.model_summary.ModelSummary static method) (cobra.summary.ModelSummary static method) _id (cobra.core.Object attribute) (cobra.core.object.Object attribute) (cobra.Object attribute) _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) _kind (cobra.core.Group attribute) (cobra.core.group.Group attribute) _lower_bound (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.Reaction attribute) _members (cobra.core.Group attribute) (cobra.core.group.Group attribute) _metabolite (cobra.summary.metabolite_summary.MetaboliteSummary attribute) _metabolite_from_dict() (in module cobra.io.dict) _metabolite_to_dict() (in module cobra.io.dict) _metabolites (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.Reaction attribute) _model (cobra.core.Group attribute) (cobra.core.group.Group attribute) (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.core.Species attribute) (cobra.core.species.Species attribute) (cobra.Reaction attribute) (cobra.Species attribute) _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) _NOT_MASS_BALANCED_TERMS (in module cobra.manipulation.validate) _number_to_chr() (in module cobra.io.sbml) _objective (cobra.summary.model_summary.ModelSummary attribute) (cobra.summary.ModelSummary attribute) _objective_value (cobra.summary.model_summary.ModelSummary attribute) (cobra.summary.ModelSummary attribute) _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) _pool (cobra.util.process_pool.ProcessPool attribute) (cobra.util.ProcessPool attribute) _populate_solver() (cobra.core.Model method) (cobra.core.model.Model method) (cobra.Model method) _progress (cobra.io.AbstractModelRepository attribute) (cobra.io.web.abstract_model_repository.AbstractModelRepository attribute) (cobra.io.web.AbstractModelRepository attribute) _project() (in module cobra.flux_analysis.fast_snp) _pubmed_re (in module cobra.io.mat) _punctuation_re (in module cobra.io.mat) _random_point() (cobra.sampling.hr_sampler.HRSampler method) (cobra.sampling.HRSampler method) _reaction (cobra.core.Species attribute) (cobra.core.species.Species attribute) (cobra.Species attribute) (cobra.summary.reaction_summary.ReactionSummary attribute) (cobra.summary.ReactionSummary attribute) _reaction_deletion() (in module cobra.flux_analysis.deletion) _reaction_deletion_worker() (in module cobra.flux_analysis.deletion) _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.summary.metabolite_summary.MetaboliteSummary attribute) _Renamer (class in cobra.manipulation.modify) _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.gene.GPR method) (cobra.core.GPR 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) _result (cobra.flux_analysis.deletion.KnockoutAccessor attribute) _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) _sbo_re (in module cobra.io.mat) _seed (cobra.sampling.hr_sampler.HRSampler attribute) (cobra.sampling.HRSampler attribute) _set_default_cache_directory() (cobra.Configuration method) (cobra.core.Configuration method) (cobra.core.configuration.Configuration method) _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) _solve_snv() (in module cobra.flux_analysis.fast_snp) _solver (cobra.Configuration attribute) (cobra.core.Configuration attribute) (cobra.core.configuration.Configuration attribute) _string_flux() (cobra.summary.reaction_summary.ReactionSummary method) (cobra.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.model_summary.ModelSummary static method) (cobra.summary.ModelSummary static method) _symbolic_gpr() (cobra.core.gene.GPR method) (cobra.core.GPR method) _tolerance (cobra.summary.Summary attribute) (cobra.summary.summary.Summary attribute) _total_components_flux() (in module cobra.flux_analysis.phenotype_phase_plane) _total_yield() (in module cobra.flux_analysis.phenotype_phase_plane) _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) _upper_bound (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.Reaction attribute) _url (cobra.io.AbstractModelRepository attribute) (cobra.io.web.abstract_model_repository.AbstractModelRepository attribute) (cobra.io.web.AbstractModelRepository attribute) _valid_atoms() (in module cobra.util) (in module cobra.util.solver) _validate() (cobra.flux_analysis.deletion.KnockoutAccessor static method) A AbstractModelRepository (class in cobra.io) (class in cobra.io.web) (class in cobra.io.web.abstract_model_repository) 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_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_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) annotation (cobra.core.Object property) (cobra.core.object.Object property) (cobra.Object property) annotations_to_mat() (in module cobra.io.mat) append() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.DictList method) as_symbolic() (cobra.core.gene.GPR method) (cobra.core.GPR 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) AutoVivification (class in cobra.util) (class in cobra.util.util) B b (cobra.sampling.hr_sampler.Problem attribute) batch() (cobra.sampling.hr_sampler.HRSampler method) (cobra.sampling.HRSampler method) BiGGModels (class in cobra.io) (class in cobra.io.web) (class in cobra.io.web.bigg_models_repository) BioModels (class in cobra.io) (class in cobra.io.web) (class in cobra.io.web.biomodels_repository) BioModelsFile (class in cobra.io.web.biomodels_repository) BioModelsFilesResponse (class in cobra.io.web.biomodels_repository) body (cobra.core.gene.GPR attribute) (cobra.core.GPR attribute) 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.Configuration property) (cobra.core.Configuration attribute) (cobra.core.Configuration property) (cobra.core.configuration.Configuration attribute) (cobra.core.configuration.Configuration property) (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) (cobra.sampling.hr_sampler.Problem attribute) bounds_tol (cobra.sampling.hr_sampler.HRSampler attribute), [1] (cobra.sampling.HRSampler attribute), [1] 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 cache_directory (cobra.Configuration attribute) (cobra.Configuration property) (cobra.core.Configuration attribute) (cobra.core.Configuration property) (cobra.core.configuration.Configuration attribute) (cobra.core.configuration.Configuration property) cache_expiration (cobra.Configuration attribute), [1] (cobra.core.Configuration attribute), [1] (cobra.core.configuration.Configuration attribute), [1] center (cobra.sampling.achr.ACHRSampler attribute) (cobra.sampling.ACHRSampler attribute) (cobra.sampling.optgp.OptGPSampler attribute), [1] (cobra.sampling.OptGPSampler attribute), [1] charge (cobra.core.Metabolite attribute) (cobra.core.metabolite.Metabolite attribute) (cobra.Metabolite 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() (in module cobra.util) (in module cobra.util.solver) check_solver_status() (in module cobra.util) (in module cobra.util.solver) choose_solver() (in module cobra.util) (in module cobra.util.solver) close() (cobra.util.process_pool.ProcessPool method) (cobra.util.ProcessPool method) 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.data module cobra.exceptions module cobra.flux_analysis module cobra.flux_analysis.deletion module cobra.flux_analysis.fast_snp module cobra.flux_analysis.fastcc module cobra.flux_analysis.find_cyclic_reactions 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.web module cobra.io.web.abstract_model_repository module cobra.io.web.bigg_models_repository module cobra.io.web.biomodels_repository module cobra.io.web.cobrapy_repository module cobra.io.web.load 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.core 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.util module cobra.util.array module cobra.util.context module cobra.util.process_pool module cobra.util.solver module cobra.util.util module CobraObject (in module cobra.core.dictlist) Cobrapy (class in cobra.io.web.cobrapy_repository) CobraSBMLError CobraYAML (class in cobra.io.yaml) compartment (cobra.core.Metabolite attribute) (cobra.core.metabolite.Metabolite attribute) (cobra.Metabolite attribute) compartment_finder (in module cobra.core.reaction) compartment_shortlist (in module cobra.medium.annotations) 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) Components (class in cobra.util) (class in cobra.util.solver) CONFIDENCE_STR (in module cobra.io.mat) config (in module cobra.core.reaction) (in module cobra.io.sbml) Configuration (class in cobra) (class in cobra.core) (class in cobra.core.configuration) configuration (in module cobra.core.model) (in module cobra.flux_analysis.deletion) (in module cobra.flux_analysis.variability) (in module cobra.io.web.load) CONS_VARS (in module cobra.util) (in module cobra.util.solver) 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) consuming_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute), [1] copy() (cobra.core.gene.GPR method) (cobra.core.GPR method) (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) costs (cobra.flux_analysis.gapfilling.GapFiller attribute), [1] create_mat_dict() (in module cobra.io.mat) create_stoichiometric_matrix() (in module cobra.util) (in module cobra.util.array) D DEFAULT_REPOSITORIES (in module cobra.io.web.load) 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) DICT_GENE (in module cobra.io.mat) DICT_GENE_REV (in module cobra.io.mat) DICT_MET (in module cobra.io.mat) DICT_MET_NOTES (in module cobra.io.mat) DICT_MET_NOTES_REV (in module cobra.io.mat) DICT_MET_REV (in module cobra.io.mat) DICT_REACTION (in module cobra.io.mat) DICT_REACTION_NOTES (in module cobra.io.mat) DICT_REACTION_NOTES_REV (in module cobra.io.mat) DICT_REACTION_REV (in module cobra.io.mat) DICT_REPLACE (in module cobra.io.mat) 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) dump() (cobra.io.yaml.CobraYAML method) E element_re (in module cobra.core.formula) (in module cobra.core.metabolite) elements (cobra.core.formula.Formula attribute) (cobra.core.Metabolite property) (cobra.core.metabolite.Metabolite property) (cobra.Metabolite property) elements_and_molecular_weights (in module cobra.core.formula) equalities (cobra.sampling.hr_sampler.Problem attribute) escape_ID() (in module cobra.manipulation) (in module cobra.manipulation.modify) eval() (cobra.core.gene.GPR method) (cobra.core.GPR method) 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) exponent (cobra.io.sbml.Unit attribute) extend() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.DictList method) extend_model() (cobra.flux_analysis.gapfilling.GapFiller method) F 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), [1] (cobra.sampling.HRSampler attribute), [1] FeasibleButNotOptimal 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_cyclic_reactions() (in module cobra.flux_analysis) (in module cobra.flux_analysis.find_cyclic_reactions) 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) 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), [1] (cobra.core.solution.Solution attribute), [1] (cobra.Solution attribute), [1] format_long_string() (in module cobra.util) (in module cobra.util.util) Formula (class in cobra.core.formula) formula (cobra.core.formula.Formula attribute) (cobra.core.Metabolite attribute) (cobra.core.metabolite.Metabolite attribute) (cobra.Metabolite attribute) 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_string() (cobra.core.gene.GPR class method) (cobra.core.GPR class method) from_symbolic() (cobra.core.gene.GPR class method) (cobra.core.GPR class method) 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) fwd_idx (cobra.sampling.achr.ACHRSampler attribute) (cobra.sampling.ACHRSampler attribute) (cobra.sampling.hr_sampler.HRSampler attribute), [1] (cobra.sampling.HRSampler attribute), [1] (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_MATLAB_TO_PROVIDERS (in module cobra.io.mat) gene_name_reaction_rule (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) GENE_PROVIDERS_TO_MATLAB (in module cobra.io.mat) gene_reaction_rule (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) gene_set (cobra.core.gene.GPRCleaner attribute) (cobra.core.gene.GPRWalker attribute) generate_fva_warmup() (cobra.sampling.hr_sampler.HRSampler method) (cobra.sampling.HRSampler method) genes (cobra.core.gene.GPR property) (cobra.core.GPR property) (cobra.core.Model attribute) (cobra.core.model.Model attribute) (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Model attribute) (cobra.Reaction property) geometric_fba() (in module cobra.flux_analysis) (in module cobra.flux_analysis.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_context() (in module cobra.util), [1] (in module cobra.util.context) get_model_from_gzip_sbml() (in module cobra.io.web.load) get_primal_by_id (cobra.core.Solution attribute) (cobra.core.solution.Solution attribute) (cobra.Solution attribute) get_sbml() (cobra.io.AbstractModelRepository method) (cobra.io.BiGGModels method) (cobra.io.BioModels method) (cobra.io.web.abstract_model_repository.AbstractModelRepository method) (cobra.io.web.AbstractModelRepository method) (cobra.io.web.bigg_models_repository.BiGGModels method) (cobra.io.web.BiGGModels method) (cobra.io.web.BioModels method) (cobra.io.web.biomodels_repository.BioModels method) (cobra.io.web.cobrapy_repository.Cobrapy method) get_solution() (in module cobra.core) (in module cobra.core.solution) get_solver_name() (in module cobra.util) (in module cobra.util.solver) GPR (class in cobra.core) (class in cobra.core.gene) gpr (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) GPRCleaner (class in cobra.core.gene) GPRWalker (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 (cobra.sampling.hr_sampler.Problem attribute) 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) indicators (cobra.flux_analysis.gapfilling.GapFiller attribute), [1] inequalities (cobra.sampling.hr_sampler.Problem attribute) Infeasible insert() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.DictList method) integer_threshold (cobra.flux_analysis.gapfilling.GapFiller attribute) interface_to_str() (in module cobra.util) (in module cobra.util.solver) is_boundary_type() (in module cobra.medium) (in module cobra.medium.boundary_types) J JSON_SPEC (in module cobra.io.json) K keyword_re (in module cobra.core.gene) keywords (in module cobra.core.gene) kind (cobra.core.Group property) (cobra.core.group.Group property) (cobra.io.sbml.Unit attribute) 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) knock_out_model_genes() (in module cobra.manipulation) (in module cobra.manipulation.delete) KnockoutAccessor (class in cobra.flux_analysis.deletion) L LARGE_VALUE (in module cobra.flux_analysis.fastcc) 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) 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_model() (in module cobra.io) (in module cobra.io.web) (in module cobra.io.web.load) load_yaml_model() (in module cobra.io) (in module cobra.io.yaml) logger (in module cobra.core.gene) (in module cobra.core.model) (in module cobra.flux_analysis.fastcc) (in module cobra.flux_analysis.gapfilling) (in module cobra.flux_analysis.geometric) (in module cobra.flux_analysis.variability) (in module cobra.io.mat) LOGGER (in module cobra.io.sbml) logger (in module cobra.io.web.load) (in module cobra.manipulation.delete) (in module cobra.medium.boundary_types) (in module cobra.medium.minimal_medium) (in module cobra.sampling.core) (in module cobra.sampling.hr_sampler) (in module cobra.summary.metabolite_summary) (in module cobra.summary.model_summary) (in module cobra.summary.reaction_summary) (in module cobra.summary.summary) (in module cobra.util) (in module cobra.util.solver) 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), [1] (cobra.core.Configuration attribute), [1] (cobra.core.configuration.Configuration attribute), [1] (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.flux_analysis.gapfilling.GapFiller attribute) (cobra.Reaction property) LOWER_BOUND_ID (in module cobra.io.sbml) lower_constraint (cobra.util.Components attribute) (cobra.util.solver.Components attribute) M main (cobra.io.web.biomodels_repository.BioModelsFilesResponse attribute) mat_parse_annotations() (in module cobra.io.mat) mat_parse_notes() (in module cobra.io.mat) max_cache_size (cobra.Configuration attribute), [1] (cobra.core.Configuration attribute), [1] (cobra.core.configuration.Configuration attribute), [1] MAX_TRIES (in module cobra.sampling.core) medium (cobra.core.Model property) (cobra.core.model.Model property) (cobra.Model property) members (cobra.core.Group property) (cobra.core.group.Group property) merge() (cobra.core.Model method) (cobra.core.model.Model method) (cobra.Model method) MET_MATLAB_TO_NOTES (in module cobra.io.mat) MET_MATLAB_TO_PROVIDERS (in module cobra.io.mat) MET_NOTES_TO_MATLAB (in module cobra.io.mat) MET_PROVIDERS_TO_MATLAB (in module cobra.io.mat) Metabolite (class in cobra) (class in cobra.core) (class in cobra.core.metabolite) metabolites (cobra.core.Model attribute) (cobra.core.model.Model attribute) (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Model attribute) (cobra.Reaction property) MetaboliteSummary (class in cobra.summary.metabolite_summary) minimal_medium() (in module cobra.medium) (in module cobra.medium.minimal_medium) Model (class in cobra) (class in cobra.core) (class in cobra.core.model) model (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.core.Species property) (cobra.core.species.Species property) (cobra.flux_analysis.gapfilling.GapFiller attribute) (cobra.Reaction property) (cobra.sampling.hr_sampler.HRSampler attribute) (cobra.sampling.HRSampler attribute) (cobra.Species property) model_from_dict() (in module cobra.io) (in module cobra.io.dict) model_to_dict() (in module cobra.io) (in module cobra.io.dict) ModelSummary (class in cobra.summary) (class in cobra.summary.model_summary) module cobra cobra.core cobra.core.configuration cobra.core.dictlist cobra.core.formula cobra.core.gene cobra.core.group cobra.core.metabolite cobra.core.model cobra.core.object cobra.core.reaction cobra.core.singleton cobra.core.solution cobra.core.species cobra.data cobra.exceptions cobra.flux_analysis cobra.flux_analysis.deletion cobra.flux_analysis.fast_snp cobra.flux_analysis.fastcc cobra.flux_analysis.find_cyclic_reactions cobra.flux_analysis.gapfilling cobra.flux_analysis.geometric cobra.flux_analysis.helpers cobra.flux_analysis.loopless cobra.flux_analysis.moma cobra.flux_analysis.parsimonious cobra.flux_analysis.phenotype_phase_plane cobra.flux_analysis.reaction cobra.flux_analysis.room cobra.flux_analysis.variability cobra.io cobra.io.dict cobra.io.json cobra.io.mat cobra.io.sbml cobra.io.web cobra.io.web.abstract_model_repository cobra.io.web.bigg_models_repository cobra.io.web.biomodels_repository cobra.io.web.cobrapy_repository cobra.io.web.load cobra.io.yaml cobra.manipulation cobra.manipulation.annotate cobra.manipulation.delete cobra.manipulation.modify cobra.manipulation.validate cobra.medium cobra.medium.annotations cobra.medium.boundary_types cobra.medium.minimal_medium cobra.sampling cobra.sampling.achr cobra.sampling.core cobra.sampling.hr_sampler cobra.sampling.optgp cobra.sampling.sampling cobra.summary cobra.summary.metabolite_summary cobra.summary.model_summary cobra.summary.reaction_summary cobra.summary.summary cobra.util cobra.util.array cobra.util.context cobra.util.process_pool cobra.util.solver cobra.util.util moma() (in module cobra.flux_analysis) (in module cobra.flux_analysis.moma) multiplier (cobra.io.sbml.Unit attribute) N n_samples (cobra.sampling.achr.ACHRSampler attribute) (cobra.sampling.ACHRSampler attribute) (cobra.sampling.hr_sampler.HRSampler attribute), [1] (cobra.sampling.HRSampler attribute), [1] (cobra.sampling.optgp.OptGPSampler attribute) (cobra.sampling.OptGPSampler attribute) name (cobra.core.Object attribute) (cobra.core.object.Object attribute) (cobra.io.AbstractModelRepository attribute), [1] (cobra.io.BiGGModels attribute), [1] (cobra.io.BioModels attribute), [1] (cobra.io.web.abstract_model_repository.AbstractModelRepository attribute), [1] (cobra.io.web.AbstractModelRepository attribute), [1] (cobra.io.web.bigg_models_repository.BiGGModels attribute), [1] (cobra.io.web.BiGGModels attribute), [1] (cobra.io.web.BioModels attribute), [1] (cobra.io.web.biomodels_repository.BioModels attribute), [1] (cobra.io.web.biomodels_repository.BioModelsFile attribute) (cobra.io.web.cobrapy_repository.Cobrapy attribute) (cobra.Object attribute) normalize_cutoff() (in module cobra.flux_analysis.helpers) notes (cobra.core.Object attribute) (cobra.core.object.Object attribute) (cobra.Object attribute) notes_to_mat() (in module cobra.io.mat) nullspace (cobra.sampling.hr_sampler.Problem attribute) nullspace() (in module cobra.util) (in module cobra.util.array) nullspace_fast_snp() (in module cobra.flux_analysis) (in module cobra.flux_analysis.fast_snp) number_start_re (in module cobra.core.gene) O Object (class in cobra) (class in cobra.core) (class in cobra.core.object) 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), [1] (cobra.core.solution.Solution attribute), [1] (cobra.Solution attribute), [1] 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_TO_EXCEPTIONS_DICT (in module cobra.exceptions) (in module cobra.util) original_model (cobra.flux_analysis.gapfilling.GapFiller attribute) 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) penalties (cobra.flux_analysis.gapfilling.GapFiller attribute) pfba() (in module cobra.flux_analysis) (in module cobra.flux_analysis.parsimonious) 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 (class in cobra.sampling.hr_sampler) problem (cobra.core.Model property) (cobra.core.model.Model property) (cobra.Model property) (cobra.sampling.achr.ACHRSampler attribute) (cobra.sampling.ACHRSampler attribute) (cobra.sampling.hr_sampler.HRSampler attribute), [1] (cobra.sampling.HRSampler attribute), [1] (cobra.sampling.optgp.OptGPSampler attribute) (cobra.sampling.OptGPSampler attribute) processes (cobra.Configuration attribute), [1] (cobra.core.Configuration attribute), [1] (cobra.core.configuration.Configuration attribute), [1] ProcessPool (class in cobra.util) (class in cobra.util.process_pool) producing_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute), [1] 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) (in module cobra.manipulation.delete) prune_unused_reactions() (in module cobra.manipulation) (in module cobra.manipulation.delete) 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 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) reactions (cobra.core.Model attribute) (cobra.core.model.Model attribute) (cobra.core.Species property) (cobra.core.species.Species property) (cobra.Model attribute) (cobra.Species property) ReactionSummary (class in cobra.summary) (class in cobra.summary.reaction_summary) read_sbml_model() (in module cobra.io) (in module cobra.io.sbml) reduced_cost (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) reduced_costs (cobra.core.Solution attribute), [1] (cobra.core.solution.Solution attribute), [1] (cobra.Solution attribute), [1] 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.Metabolite method) (cobra.core.metabolite.Metabolite method) (cobra.core.Reaction method) (cobra.core.reaction.Reaction 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_dict (cobra.manipulation.modify._Renamer attribute) rename_genes() (in module cobra.manipulation) (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), [1] (cobra.sampling.HRSampler attribute), [1] (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), [1] (cobra.sampling.HRSampler attribute), [1] (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) RXN_MATLAB_TO_NOTES (in module cobra.io.mat) RXN_MATLAB_TO_PROVIDERS (in module cobra.io.mat) RXN_NOTES_TO_MATLAB (in module cobra.io.mat) RXN_PROVIDERS_TO_MATLAB (in module cobra.io.mat) S 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) scale (cobra.io.sbml.Unit attribute) scipy_sparse (in module cobra.io.mat) secretion_flux (cobra.summary.model_summary.ModelSummary attribute), [1] (cobra.summary.ModelSummary attribute), [1] 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), [1] (cobra.core.solution.Solution attribute), [1] (cobra.Solution attribute), [1] 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.io.web.biomodels_repository.BioModelsFile attribute) size() (cobra.util.context.HistoryManager method) (cobra.util.HistoryManager method) slim_optimize() (cobra.core.Model method) (cobra.core.model.Model method) (cobra.Model method) Solution (class in cobra) (class in cobra.core) (class in cobra.core.solution) solver (cobra.Configuration attribute) (cobra.Configuration property) (cobra.core.Configuration attribute) (cobra.core.Configuration property) (cobra.core.configuration.Configuration attribute) (cobra.core.configuration.Configuration property) (cobra.core.Model property) (cobra.core.model.Model property) (cobra.Model property) 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) status (cobra.core.Solution attribute), [1] (cobra.core.solution.Solution attribute), [1] (cobra.Solution attribute), [1] step() (in module cobra.sampling) (in module cobra.sampling.core) subsystem (cobra.core.Reaction attribute) (cobra.core.reaction.Reaction attribute) (cobra.Reaction attribute) 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 target_genes (cobra.manipulation.delete._GeneRemover attribute) thinning (cobra.sampling.hr_sampler.HRSampler attribute) (cobra.sampling.HRSampler attribute) 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.model_summary.ModelSummary method) (cobra.summary.ModelSummary method) (cobra.summary.reaction_summary.ReactionSummary method) (cobra.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.core.gene.GPR method) (cobra.core.GPR method) (cobra.summary.metabolite_summary.MetaboliteSummary method) (cobra.summary.model_summary.ModelSummary method) (cobra.summary.ModelSummary method) (cobra.summary.reaction_summary.ReactionSummary method) (cobra.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), [1] (cobra.core.Configuration attribute), [1] (cobra.core.configuration.Configuration attribute), [1] (cobra.core.Model property) (cobra.core.model.Model property) (cobra.Model property) (cobra.summary.Summary property) (cobra.summary.summary.Summary property) U Unbounded UndefinedSolution union() (cobra.core.DictList method) (cobra.core.dictlist.DictList method) (cobra.DictList method) Unit (class in cobra.io.sbml) UNITS_FLUX (in module cobra.io.sbml) universal (cobra.flux_analysis.gapfilling.GapFiller attribute) update_costs() (cobra.flux_analysis.gapfilling.GapFiller method) update_genes() (cobra.core.gene.GPR method) (cobra.core.GPR method) update_genes_from_gpr() (cobra.core.Reaction method) (cobra.core.reaction.Reaction method) (cobra.Reaction method) update_variable_bounds() (cobra.core.Reaction method) (cobra.core.reaction.Reaction method) (cobra.Reaction method) upper_bound (cobra.Configuration attribute), [1] (cobra.core.Configuration attribute), [1] (cobra.core.configuration.Configuration attribute), [1] (cobra.core.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) UPPER_BOUND_ID (in module cobra.io.sbml) upper_constraint (cobra.util.Components attribute) (cobra.util.solver.Components attribute) uptake_flux (cobra.summary.model_summary.ModelSummary attribute), [1] (cobra.summary.ModelSummary attribute), [1] url (cobra.io.AbstractModelRepository property) (cobra.io.web.abstract_model_repository.AbstractModelRepository property) (cobra.io.web.AbstractModelRepository property) 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 (cobra.util.Components attribute) (cobra.util.solver.Components attribute) variable_bounds (cobra.sampling.hr_sampler.Problem attribute) variable_fixed (cobra.sampling.hr_sampler.Problem attribute) variables (cobra.core.Model property) (cobra.core.model.Model property) (cobra.Model property) visit_BinOp() (cobra.core.gene.GPRCleaner method) visit_BoolOp() (cobra.core.gene.GPRWalker method) (cobra.manipulation.delete._GeneRemover method) visit_Name() (cobra.core.gene.GPRCleaner method) (cobra.core.gene.GPRWalker method) (cobra.manipulation.delete._GeneRemover method) (cobra.manipulation.modify._GeneEscaper method) (cobra.manipulation.modify._Renamer method) W warmup (cobra.sampling.achr.ACHRSampler attribute) (cobra.sampling.ACHRSampler attribute) (cobra.sampling.hr_sampler.HRSampler attribute), [1] (cobra.sampling.HRSampler attribute), [1] (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.Reaction property) (cobra.core.reaction.Reaction property) (cobra.Reaction property) Y 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) yaml (in module cobra.io.yaml) YAML_SPEC (in module cobra.io.yaml) Z ZERO_BOUND_ID (in module cobra.io.sbml)