cobra
0.25.0
1. Getting Started
2. Global Configuration
3. Building a Model
4. Reading and Writing Models
5. Simulating with FBA
6. Simulating Deletions
7. Production envelopes
8. Flux sampling
9. Loopless FBA
10. Consistency testing
11. Gapfillling
12. Growth media
13. Solvers
14. Tailored constraints, variables and objectives
15. Dynamic Flux Balance Analysis (dFBA) in COBRApy
16. FAQ
17. API Reference
cobra
Docs
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Index
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Index
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C
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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)
__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.LegacySolution method)
(cobra.core.Solution method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.DictList method)
(cobra.flux_analysis.deletion.KnockoutAccessor method)
(cobra.Solution method)
(cobra.util.AutoVivification method)
(cobra.util.util.AutoVivification method)
__getslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__getstate__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Species method)
(cobra.core.species.Species method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Object method)
(cobra.sampling.optgp.OptGPSampler method)
(cobra.sampling.OptGPSampler method)
(cobra.Species method)
__iadd__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__imul__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__isub__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Reaction method)
__len__() (cobra.core.Group method)
(cobra.core.group.Group method)
__mul__() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
__radd__ (cobra.core.Reaction attribute)
(cobra.core.reaction.Reaction attribute)
(cobra.Reaction attribute)
__reduce__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__repr__() (cobra.Configuration method)
(cobra.core.Configuration method)
(cobra.core.configuration.Configuration method)
(cobra.core.gene.GPR method)
(cobra.core.GPR method)
(cobra.core.LegacySolution method)
(cobra.core.Object method)
(cobra.core.object.Object method)
(cobra.core.Solution method)
(cobra.core.solution.LegacySolution method)
(cobra.core.solution.Solution method)
(cobra.Object method)
(cobra.Solution method)
__setitem__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__setslice__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
__setstate__() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.DictList method)
(cobra.Model method)
(cobra.Reaction method)
__single_iteration() (cobra.sampling.achr.ACHRSampler method)
(cobra.sampling.ACHRSampler method)
__str__() (cobra.core.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)
_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)
_bounds_dist() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_bracket_re (in module cobra.io.mat)
_cached_load() (in module cobra.io.web.load)
_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_parameter() (in module cobra.io.sbml)
_display_flux() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
_dissociate_gene() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
_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)
_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)
_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)
_gene_to_dict() (in module cobra.io.dict)
_GeneEscaper (class in cobra.manipulation.modify)
_generate() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
_generate_index() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
_GeneRemover (class in cobra.manipulation.delete)
_get_doc_from_filename() (in module cobra.io.sbml)
_get_growth() (in module cobra.flux_analysis.deletion)
_get_id_compartment() (in module cobra.io.mat)
_html_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method)
(cobra.summary.MetaboliteSummary static method)
(cobra.summary.model_summary.ModelSummary static method)
(cobra.summary.ModelSummary static method)
_init_worker() (in module cobra.flux_analysis.deletion)
(in module cobra.flux_analysis.variability)
_instances (cobra.core.singleton.Singleton attribute)
_is_redundant() (cobra.sampling.hr_sampler.HRSampler method)
(cobra.sampling.HRSampler method)
_metabolite_from_dict() (in module cobra.io.dict)
_metabolite_to_dict() (in module cobra.io.dict)
_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)
_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)
_progress (cobra.io.AbstractModelRepository attribute)
(cobra.io.web.abstract_model_repository.AbstractModelRepository attribute)
(cobra.io.web.AbstractModelRepository attribute)
_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_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)
_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)
_reverse_arrow_finder (in module cobra.core.reaction)
_reversible_arrow_finder (in module cobra.core.reaction)
_sbase_annotations() (in module cobra.io.sbml)
_sbase_notes_dict() (in module cobra.io.sbml)
_sbml_to_model() (in module cobra.io.sbml)
_set_default_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)
_string_flux() (cobra.summary.reaction_summary.ReactionSummary method)
_string_objective() (cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
_string_table() (cobra.summary.metabolite_summary.MetaboliteSummary static method)
(cobra.summary.MetaboliteSummary static method)
(cobra.summary.model_summary.ModelSummary static method)
(cobra.summary.ModelSummary static method)
_symbolic_gpr() (cobra.core.gene.GPR method)
(cobra.core.GPR method)
_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)
_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_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)
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 (in module cobra.sampling.hr_sampler)
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)
BOUND_MINUS_INF (in module cobra.io.sbml)
BOUND_PLUS_INF (in module cobra.io.sbml)
boundary() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Model property)
(cobra.Reaction property)
bounds (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(in module cobra.sampling.hr_sampler)
bounds() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
(cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
bounds_tol (cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
build_reaction_from_string() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
build_reaction_string() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
C
cache_directory (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
cache_directory() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
cache_expiration (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
center (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
check_mass_balance() (cobra.core.Reaction method)
(cobra.core.reaction.Reaction method)
(cobra.Reaction method)
(in module cobra.manipulation)
(in module cobra.manipulation.validate)
check_metabolite_compartment_formula() (in module cobra.manipulation)
(in module cobra.manipulation.validate)
check_solver() (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.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.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)
Cobrapy (class in cobra.io.web.cobrapy_repository)
CobraSBMLError
CobraYAML (class in cobra.io.yaml)
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)
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)
(cobra.summary.MetaboliteSummary attribute)
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)
create_mat_dict() (in module cobra.io.mat)
create_stoichiometric_matrix() (in module cobra.util)
(in module cobra.util.array)
D
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_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)
dress_results() (cobra.core.LegacySolution method)
(cobra.core.solution.LegacySolution method)
dump() (cobra.io.yaml.CobraYAML method)
E
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)
equalities (in module cobra.sampling.hr_sampler)
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)
extend() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
extend_model() (cobra.flux_analysis.gapfilling.GapFiller 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
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_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)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
format_long_string() (in module cobra.util)
(in module cobra.util.util)
Formula (class in cobra.core.formula)
formula_weight() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
forward_variable() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
from_json() (in module cobra.io)
(in module cobra.io.json)
from_mat_struct() (in module cobra.io.mat)
from_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)
(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_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)
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.gene.GPR property)
(cobra.core.GPR property)
(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)
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_metabolite_compartments() (cobra.core.Model method)
(cobra.core.model.Model method)
(cobra.Model method)
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 (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)
indicators (cobra.flux_analysis.gapfilling.GapFiller attribute)
inequalities (in module cobra.sampling.hr_sampler)
Infeasible
init (module)
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)
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)
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
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)
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.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)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
lower_bound() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(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)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
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.Model attribute)
metabolites() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
MetaboliteSummary (class in cobra.summary)
(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.Reaction property)
(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)
moma() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.moma)
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 (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)
normalize_cutoff() (in module cobra.flux_analysis.helpers)
notes_to_mat() (in module cobra.io.mat)
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() (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)
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)
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)
pop() (cobra.core.DictList method)
(cobra.core.dictlist.DictList method)
(cobra.DictList method)
prev (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
problem (cobra.sampling.achr.ACHRSampler attribute)
(cobra.sampling.ACHRSampler attribute)
(cobra.sampling.hr_sampler.HRSampler attribute)
(cobra.sampling.HRSampler attribute)
(cobra.sampling.optgp.OptGPSampler attribute)
(cobra.sampling.OptGPSampler attribute)
Problem (in module cobra.sampling.hr_sampler)
problem() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
processes (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
ProcessPool (class in cobra.util)
(class in cobra.util.process_pool)
producing_flux (cobra.summary.metabolite_summary.MetaboliteSummary attribute)
(cobra.summary.MetaboliteSummary attribute)
production_envelope() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.phenotype_phase_plane)
products() (cobra.core.Reaction property)
(cobra.core.reaction.Reaction property)
(cobra.Reaction property)
prune_unused_metabolites() (in module cobra.manipulation)
(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.Model attribute)
reactions() (cobra.core.Species property)
(cobra.core.species.Species property)
(cobra.Species property)
ReactionSummary (class in cobra.summary.reaction_summary)
read_sbml_model() (in module cobra.io)
(in module cobra.io.sbml)
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.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_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)
(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)
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)
scipy_sparse (in module cobra.io.mat)
secretion_flux (cobra.summary.model_summary.ModelSummary attribute)
(cobra.summary.ModelSummary attribute)
set_objective() (in module cobra.util)
(in module cobra.util.solver)
shadow_price() (cobra.core.Metabolite property)
(cobra.core.metabolite.Metabolite property)
(cobra.Metabolite property)
shadow_prices (cobra.core.Solution attribute)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
shared_np_array() (in module cobra.sampling)
(in module cobra.sampling.hr_sampler)
SHORT_LONG_DIRECTION (in module cobra.io.sbml)
show_versions() (in module cobra)
(in module cobra.util)
(in module cobra.util.util)
single_gene_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
single_reaction_deletion() (in module cobra.flux_analysis)
(in module cobra.flux_analysis.deletion)
Singleton (class in cobra.core.singleton)
sinks() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
size (cobra.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)
solution (cobra.core.Model attribute)
(cobra.core.model.Model attribute)
(cobra.Model attribute)
solver (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
(cobra.core.LegacySolution attribute)
(cobra.core.solution.LegacySolution attribute)
solver() (cobra.Configuration property)
(cobra.core.Configuration property)
(cobra.core.configuration.Configuration property)
(cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
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)
(cobra.core.solution.Solution attribute)
(cobra.Solution attribute)
step() (in module cobra.sampling)
(in module cobra.sampling.core)
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
to_frame() (cobra.core.Solution method)
(cobra.core.solution.Solution method)
(cobra.Solution method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_html() (cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_json() (in module cobra.io)
(in module cobra.io.json)
to_string() (cobra.core.gene.GPR method)
(cobra.core.GPR method)
(cobra.summary.metabolite_summary.MetaboliteSummary method)
(cobra.summary.MetaboliteSummary method)
(cobra.summary.model_summary.ModelSummary method)
(cobra.summary.ModelSummary method)
(cobra.summary.reaction_summary.ReactionSummary method)
(cobra.summary.Summary method)
(cobra.summary.summary.Summary method)
to_yaml() (in module cobra.io)
(in module cobra.io.yaml)
tolerance (cobra.Configuration attribute)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
tolerance() (cobra.core.Model property)
(cobra.core.model.Model property)
(cobra.Model property)
(cobra.summary.Summary property)
(cobra.summary.summary.Summary property)
U
Unbounded
UndefinedSolution
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_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)
(cobra.core.Configuration attribute)
(cobra.core.configuration.Configuration attribute)
upper_bound() (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)
(cobra.summary.ModelSummary attribute)
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 (in module cobra.sampling.hr_sampler)
variable_fixed (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.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)
(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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