Index

_

__add__() (cobra.core.DictList.DictList method) (cobra.core.Formula.Formula method) (cobra.core.Model.Model method) (cobra.core.Reaction.Reaction method) __contains__() (cobra.core.DictList.DictList method) __getstate__() (cobra.core.DictList.DictList method) (cobra.core.Object.Object method) (cobra.core.Species.Species method)

__iadd__() (cobra.core.DictList.DictList method) (cobra.core.Model.Model method) __imul__() (cobra.core.Reaction.Reaction method) __setstate__() (cobra.core.DictList.DictList method) (cobra.core.Model.Model method) (cobra.core.Reaction.Reaction method)

A

add_metabolites() (cobra.core.ArrayBasedModel.ArrayBasedModel method) (cobra.core.Model.Model method) (cobra.core.Reaction.Reaction method) add_reaction() (cobra.core.Model.Model method) add_reactions() (cobra.core.ArrayBasedModel.ArrayBasedModel method) (cobra.core.Model.Model method) (cobra.flux_analysis.gapfilling.SUXModelMILP method) add_sbml_species() (in module cobra.io.sbml) add_SBO() (in module cobra.manipulation.annotate) annotate_cobra_from_sbml() (in module cobra.io.sbml3) annotate_sbml_from_cobra() (in module cobra.io.sbml3)

append() (cobra.core.DictList.DictList method) ArrayBasedModel (class in cobra.core.ArrayBasedModel) assess() (in module cobra.flux_analysis.reaction) assess_medium_component_essentiality() (in module cobra.flux_analysis.essentiality) assess_precursors() (in module cobra.flux_analysis.reaction) assess_products() (in module cobra.flux_analysis.reaction) ast2str() (in module cobra.core.Gene)

B

b (cobra.core.ArrayBasedModel.ArrayBasedModel attribute) Basic (class in cobra.io.sbml3) boundary (cobra.core.Reaction.Reaction attribute)

build_reaction_from_string() (cobra.core.Reaction.Reaction method) build_reaction_string() (cobra.core.Reaction.Reaction method)

C

calculate_lp_variability() (in module cobra.flux_analysis.variability) calculate_phenotype_phase_plane() (in module cobra.flux_analysis.phenotype_phase_plane) canonical_form() (in module cobra.manipulation.modify) change_objective() (cobra.core.Model.Model method) check_mass_balance() (cobra.core.Reaction.Reaction method) (in module cobra.manipulation.validate) check_metabolite_compartment_formula() (in module cobra.manipulation.validate) check_reaction_bounds() (in module cobra.manipulation.validate) clear_metabolites() (cobra.core.Reaction.Reaction method) clip() (in module cobra.io.sbml3) cobra (module) cobra.core (module) cobra.core.ArrayBasedModel (module) cobra.core.DictList (module) cobra.core.Formula (module) cobra.core.Gene (module) cobra.core.Metabolite (module) cobra.core.Model (module) cobra.core.Object (module) cobra.core.Reaction (module) cobra.core.Solution (module) cobra.core.Species (module) cobra.design (module) cobra.design.design_algorithms (module) cobra.flux_analysis (module) cobra.flux_analysis.deletion_worker (module) cobra.flux_analysis.double_deletion (module) cobra.flux_analysis.essentiality (module) cobra.flux_analysis.gapfilling (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.single_deletion (module) cobra.flux_analysis.variability (module) cobra.io (module) cobra.io.json (module) cobra.io.mat (module) cobra.io.sbml (module) cobra.io.sbml3 (module) cobra.manipulation (module) cobra.manipulation.annotate (module) cobra.manipulation.delete (module) cobra.manipulation.modify (module) cobra.manipulation.validate (module) cobra.topology (module) cobra.topology.reporter_metabolites (module) CobraDeletionMockPool (class in cobra.flux_analysis.deletion_worker) CobraDeletionPool (class in cobra.flux_analysis.deletion_worker) CobraSBMLError compute_fba_deletion() (in module cobra.flux_analysis.deletion_worker) compute_fba_deletion_worker() (in module cobra.flux_analysis.deletion_worker) constraint_sense (cobra.core.ArrayBasedModel.ArrayBasedModel attribute) construct_gpr_xml() (in module cobra.io.sbml3) construct_loopless_model() (in module cobra.flux_analysis.loopless) convert_to_irreversible() (in module cobra.manipulation.modify) copy() (cobra.core.ArrayBasedModel.ArrayBasedModel method) (cobra.core.Model.Model method) (cobra.core.Reaction.Reaction method) (cobra.core.Species.Species method) create_cobra_model_from_sbml_file() (in module cobra.io.sbml) create_euclidian_distance_lp() (in module cobra.flux_analysis.moma) create_euclidian_distance_objective() (in module cobra.flux_analysis.moma) create_euclidian_moma_model() (in module cobra.flux_analysis.moma) create_mat_dict() (in module cobra.io.mat)

D

delete() (cobra.core.Reaction.Reaction method) delete_model_genes() (in module cobra.manipulation.delete) description (cobra.core.Model.Model attribute) DictList (class in cobra.core.DictList) double_deletion() (in module cobra.flux_analysis.double_deletion)

double_gene_deletion() (in module cobra.flux_analysis.double_deletion) double_reaction_deletion() (in module cobra.flux_analysis.double_deletion) dress_results() (cobra.core.Solution.Solution method) dual_problem() (in module cobra.design.design_algorithms)

E

elements (cobra.core.Metabolite.Metabolite attribute) escape_ID() (in module cobra.manipulation.modify)

eval_gpr() (in module cobra.core.Gene) extend() (cobra.core.DictList.DictList method)

F

find_blocked_reactions() (in module cobra.flux_analysis.variability) find_gene_knockout_reactions() (in module cobra.manipulation.delete) fix_legacy_id() (in module cobra.io.sbml) flux_variability_analysis() (in module cobra.flux_analysis.variability) format_results_frame() (in module cobra.flux_analysis.double_deletion)

Formula (class in cobra.core.Formula) formula_weight (cobra.core.Metabolite.Metabolite attribute) from_json() (in module cobra.io.json) from_mat_struct() (in module cobra.io.mat) Frozendict (class in cobra.core.Reaction)

G

Gene (class in cobra.core.Gene) gene_name_reaction_rule (cobra.core.Reaction.Reaction attribute) gene_reaction_rule (cobra.core.Reaction.Reaction attribute) generate_matrix_indexes() (in module cobra.flux_analysis.double_deletion) genes (cobra.core.Reaction.Reaction attribute) get_attrib() (in module cobra.io.sbml3) get_by_id() (cobra.core.DictList.DictList method)

get_coefficient() (cobra.core.Reaction.Reaction method) get_coefficients() (cobra.core.Reaction.Reaction method) get_compartments() (cobra.core.Reaction.Reaction method) get_compiled_gene_reaction_rules() (in module cobra.manipulation.delete) get_libsbml_document() (in module cobra.io.sbml) GPRCleaner (class in cobra.core.Gene) growMatch() (in module cobra.flux_analysis.gapfilling)

H

has_id() (cobra.core.DictList.DictList method)

I

identify_reporter_metabolites() (in module cobra.topology.reporter_metabolites) indent_xml() (in module cobra.io.sbml3) index() (cobra.core.DictList.DictList method)

initialize_growth_medium() (in module cobra.manipulation.modify) insert() (cobra.core.DictList.DictList method)

K

knock_out() (cobra.core.Reaction.Reaction method)

L

list_attr() (cobra.core.DictList.DictList method) load_json_model() (in module cobra.io.json)

load_matlab_model() (in module cobra.io.mat) lower_bounds (cobra.core.ArrayBasedModel.ArrayBasedModel attribute)

M

Metabolite (class in cobra.core.Metabolite) metabolites (cobra.core.Reaction.Reaction attribute) Model (class in cobra.core.Model) model (cobra.core.Reaction.Reaction attribute) (cobra.core.Species.Species attribute)

model_to_pymatbridge() (in module cobra.io.mat) model_to_xml() (in module cobra.io.sbml3) moma() (in module cobra.flux_analysis.moma) moma_knockout() (in module cobra.flux_analysis.moma)

N

ns() (in module cobra.io.sbml3)

O

Object (class in cobra.core.Object) objective (cobra.core.Model.Model attribute) objective_coefficients (cobra.core.ArrayBasedModel.ArrayBasedModel attribute)

optimize() (cobra.core.Model.Model method) optimize_minimal_flux() (in module cobra.flux_analysis.parsimonious)

P

parse_composition() (cobra.core.Formula.Formula method) parse_gpr() (in module cobra.core.Gene) parse_legacy_id() (in module cobra.io.sbml) parse_legacy_sbml_notes() (in module cobra.io.sbml) parse_stream() (in module cobra.io.sbml3) parse_xml_into_model() (in module cobra.io.sbml3) phenotypePhasePlaneData (class in cobra.flux_analysis.phenotype_phase_plane) pids (cobra.flux_analysis.deletion_worker.CobraDeletionPool attribute)

plot() (cobra.flux_analysis.phenotype_phase_plane.phenotypePhasePlaneData method) plot_matplotlib() (cobra.flux_analysis.phenotype_phase_plane.phenotypePhasePlaneData method) plot_mayavi() (cobra.flux_analysis.phenotype_phase_plane.phenotypePhasePlaneData method) pop() (cobra.core.DictList.DictList method) (cobra.core.Reaction.Frozendict method) (cobra.core.Reaction.Reaction method) popitem() (cobra.core.Reaction.Frozendict method) products (cobra.core.Reaction.Reaction attribute) prune_unused_metabolites() (in module cobra.manipulation.delete) prune_unused_reactions() (in module cobra.manipulation.delete)

Q

query() (cobra.core.DictList.DictList method)

R

reactants (cobra.core.Reaction.Reaction attribute) Reaction (class in cobra.core.Reaction) reaction (cobra.core.Reaction.Reaction attribute) reactions (cobra.core.Species.Species attribute) read_legacy_sbml() (in module cobra.io.sbml) read_sbml_model() (in module cobra.io.sbml3) receive_all() (cobra.flux_analysis.deletion_worker.CobraDeletionMockPool method) (cobra.flux_analysis.deletion_worker.CobraDeletionPool method) receive_one() (cobra.flux_analysis.deletion_worker.CobraDeletionMockPool method) (cobra.flux_analysis.deletion_worker.CobraDeletionPool method) remove() (cobra.core.DictList.DictList method)

remove_from_model() (cobra.core.Gene.Gene method) (cobra.core.Metabolite.Metabolite method) (cobra.core.Reaction.Reaction method) remove_genes() (in module cobra.manipulation.delete) remove_reactions() (cobra.core.ArrayBasedModel.ArrayBasedModel method) (cobra.core.Model.Model method) repair() (cobra.core.Model.Model method) reverse() (cobra.core.DictList.DictList method) reversibility (cobra.core.Reaction.Reaction attribute) revert_to_reversible() (in module cobra.manipulation.modify) run_optknock() (in module cobra.design.design_algorithms)

S

S (cobra.core.ArrayBasedModel.ArrayBasedModel attribute) save_json_model() (in module cobra.io.json) save_matlab_model() (in module cobra.io.mat) segment() (cobra.flux_analysis.phenotype_phase_plane.phenotypePhasePlaneData method) set_attrib() (in module cobra.io.sbml3) set_up_optknock() (in module cobra.design.design_algorithms) single_deletion() (in module cobra.flux_analysis.single_deletion) single_gene_deletion() (in module cobra.flux_analysis.single_deletion) single_gene_deletion_fba() (in module cobra.flux_analysis.single_deletion) single_gene_deletion_moma() (in module cobra.flux_analysis.single_deletion) single_reaction_deletion() (in module cobra.flux_analysis.single_deletion) single_reaction_deletion_fba() (in module cobra.flux_analysis.single_deletion) single_reaction_deletion_moma() (in module cobra.flux_analysis.single_deletion)

SMILEY() (in module cobra.flux_analysis.gapfilling) Solution (class in cobra.core.Solution) solve() (cobra.flux_analysis.gapfilling.SUXModelMILP method) solve_moma_model() (in module cobra.flux_analysis.moma) sort() (cobra.core.DictList.DictList method) Species (class in cobra.core.Species) start() (cobra.flux_analysis.deletion_worker.CobraDeletionMockPool method) (cobra.flux_analysis.deletion_worker.CobraDeletionPool method) strnum() (in module cobra.io.sbml3) submit() (cobra.flux_analysis.deletion_worker.CobraDeletionMockPool method) (cobra.flux_analysis.deletion_worker.CobraDeletionPool method) subtract_metabolites() (cobra.core.Reaction.Reaction method) summary() (cobra.core.Metabolite.Metabolite method) (cobra.core.Model.Model method) SUXModelMILP (class in cobra.flux_analysis.gapfilling)

T

terminate() (cobra.flux_analysis.deletion_worker.CobraDeletionMockPool method) (cobra.flux_analysis.deletion_worker.CobraDeletionPool method) to_array_based_model() (cobra.core.Model.Model method)

to_json() (in module cobra.io.json)

U

undelete_model_genes() (in module cobra.manipulation.delete) union() (cobra.core.DictList.DictList method)

update() (cobra.core.ArrayBasedModel.ArrayBasedModel method) upper_bounds (cobra.core.ArrayBasedModel.ArrayBasedModel attribute)

V

validate_sbml_model() (in module cobra.io.sbml3) visit_BinOp() (cobra.core.Gene.GPRCleaner method)

visit_Name() (cobra.core.Gene.GPRCleaner method)

W

weight (cobra.core.Formula.Formula attribute) write_cobra_model_to_sbml_file() (in module cobra.io.sbml)

write_sbml_model() (in module cobra.io.sbml3)

X

x (cobra.core.Reaction.Reaction attribute)

Y

y (cobra.core.Metabolite.Metabolite attribute)

yield_upper_tria_indexes() (in module cobra.flux_analysis.double_deletion)