cobra
stable
1. Getting Started
2. Building a Model
3. Reading and Writing Models
4. Simulating with FBA
5. Simulating Deletions
6. Production envelopes
7. Flux sampling
8. Loopless FBA
9. Gapfillling
10. Solvers
11. Tailored constraints, variables and objectives
12. Using the COBRA toolbox with cobrapy
13. FAQ
14. cobra package
cobra
Docs
»
Index
Edit on GitHub
Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
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V
|
W
|
X
|
Y
A
ACHRSampler (class in cobra.flux_analysis.sampling)
add() (cobra.core.dictlist.DictList method)
add_absolute_expression() (in module cobra.util.solver)
add_boundary() (cobra.core.model.Model method)
add_cons_vars() (cobra.core.model.Model method)
add_cons_vars_to_problem() (in module cobra.util.solver)
add_envelope() (in module cobra.flux_analysis.phenotype_phase_plane)
add_loopless() (in module cobra.flux_analysis.loopless)
add_metabolites() (cobra.core.model.Model method)
(cobra.core.reaction.Reaction method)
add_moma() (in module cobra.flux_analysis.moma)
add_pfba() (in module cobra.flux_analysis.parsimonious)
add_reaction() (cobra.core.model.Model method)
add_reactions() (cobra.core.model.Model method)
add_sbml_species() (in module cobra.io.sbml)
add_SBO() (in module cobra.manipulation.annotate)
add_switches_and_objective() (cobra.flux_analysis.gapfilling.GapFiller method)
annotate_cobra_from_sbml() (in module cobra.io.sbml3)
annotate_sbml_from_cobra() (in module cobra.io.sbml3)
append() (cobra.core.dictlist.DictList method)
assert_optimal() (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.util)
B
b (cobra.flux_analysis.sampling.Problem attribute)
,
[1]
batch() (cobra.flux_analysis.sampling.HRSampler method)
boundary (cobra.core.reaction.Reaction attribute)
bounds (cobra.core.reaction.Reaction attribute)
(cobra.flux_analysis.sampling.Problem attribute)
,
[1]
bounds_tol (in module cobra.flux_analysis.sampling)
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)
center (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
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)
check_solver_status() (in module cobra.util.solver)
choose_solver() (in module cobra.util.solver)
clip() (in module cobra.io.sbml3)
cobra (module)
cobra.config (module)
cobra.core (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.exceptions (module)
cobra.flux_analysis (module)
cobra.flux_analysis.deletion_worker (module)
cobra.flux_analysis.double_deletion (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.sampling (module)
cobra.flux_analysis.single_deletion (module)
cobra.flux_analysis.summary (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)
cobra.util (module)
cobra.util.array (module)
cobra.util.context (module)
cobra.util.solver (module)
cobra.util.util (module)
CobraDeletionMockPool (class in cobra.flux_analysis.deletion_worker)
CobraDeletionPool (class in cobra.flux_analysis.deletion_worker)
CobraSBMLError
compartments (cobra.core.model.Model attribute)
(cobra.core.reaction.Reaction attribute)
compute_fba_deletion() (in module cobra.flux_analysis.deletion_worker)
compute_fba_deletion_worker() (in module cobra.flux_analysis.deletion_worker)
constraint (cobra.core.metabolite.Metabolite attribute)
constraint_matrices() (in module cobra.util.array)
constraints (cobra.core.model.Model 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.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)
create_mat_metabolite_id() (in module cobra.io.mat)
create_stoichiometric_matrix() (in module cobra.util.array)
D
DefunctError
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.LegacySolution method)
dual_problem() (in module cobra.design.design_algorithms)
E
elements (cobra.core.metabolite.Metabolite attribute)
equalities (cobra.flux_analysis.sampling.Problem attribute)
,
[1]
escape_ID() (in module cobra.manipulation.modify)
eval_gpr() (in module cobra.core.gene)
exchanges (cobra.core.model.Model attribute)
extend() (cobra.core.dictlist.DictList method)
extend_model() (cobra.flux_analysis.gapfilling.GapFiller method)
extract_rdf_annotation() (in module cobra.io.sbml3)
F
f (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
,
[1]
feasibility_tol (in module cobra.flux_analysis.sampling)
FeasibleButNotOptimal
fill() (cobra.flux_analysis.gapfilling.GapFiller method)
find_blocked_reactions() (in module cobra.flux_analysis.variability)
find_carbon_sources() (in module cobra.flux_analysis.phenotype_phase_plane)
find_essential_genes() (in module cobra.flux_analysis.variability)
find_essential_reactions() (in module cobra.flux_analysis.variability)
find_gene_knockout_reactions() (in module cobra.manipulation.delete)
fix_legacy_id() (in module cobra.io.sbml)
fix_objective_as_constraint() (in module cobra.util.solver)
flux (cobra.core.reaction.Reaction attribute)
flux_expression (cobra.core.reaction.Reaction attribute)
flux_variability_analysis() (in module cobra.flux_analysis.variability)
fluxes (cobra.core.solution.Solution attribute)
format_long_string() (in module cobra.util.util)
format_results_frame() (in module cobra.flux_analysis.double_deletion)
Formula (class in cobra.core.formula)
formula_weight (cobra.core.metabolite.Metabolite attribute)
forward_variable (cobra.core.reaction.Reaction attribute)
from_json() (in module cobra.io.json)
from_mat_struct() (in module cobra.io.mat)
functional (cobra.core.gene.Gene attribute)
(cobra.core.reaction.Reaction attribute)
fwd_idx (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
G
gapfill() (in module cobra.flux_analysis.gapfilling)
GapFiller (class in cobra.flux_analysis.gapfilling)
Gene (class in cobra.core.gene)
gene_name_reaction_rule (cobra.core.reaction.Reaction attribute)
gene_reaction_rule (cobra.core.reaction.Reaction attribute)
generate_fva_warmup() (cobra.flux_analysis.sampling.HRSampler method)
generate_matrix_indexes() (in module cobra.flux_analysis.double_deletion)
genes (cobra.core.model.Model attribute)
(cobra.core.reaction.Reaction attribute)
get_attrib() (in module cobra.io.sbml3)
get_by_any() (cobra.core.dictlist.DictList method)
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_context() (in module cobra.util.context)
get_libsbml_document() (in module cobra.io.sbml)
get_metabolite_compartments() (cobra.core.model.Model method)
get_primal_by_id() (cobra.core.solution.Solution method)
get_solution() (in module cobra.core.solution)
get_solver_name() (in module cobra.util.solver)
GPRCleaner (class in cobra.core.gene)
growMatch() (in module cobra.flux_analysis.gapfilling)
H
has_id() (cobra.core.dictlist.DictList method)
HistoryManager (class in cobra.util.context)
homogeneous (cobra.flux_analysis.sampling.Problem attribute)
,
[1]
HRSampler (class in cobra.flux_analysis.sampling)
I
id (cobra.core.object.Object attribute)
identify_reporter_metabolites() (in module cobra.topology.reporter_metabolites)
indent_xml() (in module cobra.io.sbml3)
index() (cobra.core.dictlist.DictList method)
inequalities (cobra.flux_analysis.sampling.Problem attribute)
,
[1]
Infeasible
insert() (cobra.core.dictlist.DictList method)
interface_to_str() (in module cobra.util.solver)
K
knock_out() (cobra.core.gene.Gene method)
(cobra.core.reaction.Reaction method)
L
LegacySolution (class in cobra.core.solution)
linear_reaction_coefficients() (in module cobra.util.solver)
list_attr() (cobra.core.dictlist.DictList method)
load_json_model() (in module cobra.io.json)
load_matlab_model() (in module cobra.io.mat)
LOGGER (in module cobra.flux_analysis.sampling)
loopless_fva_iter() (in module cobra.flux_analysis.loopless)
loopless_solution() (in module cobra.flux_analysis.loopless)
lower_bound (cobra.core.reaction.Reaction attribute)
M
medium (cobra.core.model.Model attribute)
merge() (cobra.core.model.Model method)
Metabolite (class in cobra.core.metabolite)
metabolite_summary() (in module cobra.flux_analysis.summary)
metabolites (cobra.core.model.Model attribute)
(cobra.core.reaction.Reaction attribute)
Model (class in cobra.core.model)
model (cobra.core.reaction.Reaction attribute)
(cobra.core.species.Species attribute)
(cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
model_summary() (in module cobra.flux_analysis.summary)
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)
mp_init() (in module cobra.flux_analysis.sampling)
N
n_samples (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
nproj (in module cobra.flux_analysis.sampling)
nproj_center (in module cobra.flux_analysis.sampling)
ns() (in module cobra.io.sbml3)
nullspace (cobra.flux_analysis.sampling.Problem attribute)
,
[1]
nullspace() (in module cobra.util.array)
O
Object (class in cobra.core.object)
objective (cobra.core.model.Model attribute)
objective_coefficient (cobra.core.reaction.Reaction attribute)
objective_direction (cobra.core.model.Model attribute)
objective_value (cobra.core.solution.Solution attribute)
OptGPSampler (class in cobra.flux_analysis.sampling)
OptimizationError
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)
pfba() (in module cobra.flux_analysis.parsimonious)
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)
prev (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
Problem (class in cobra.flux_analysis.sampling)
problem (cobra.core.model.Model attribute)
(cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
production_envelope() (in module cobra.flux_analysis.phenotype_phase_plane)
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)
reaction_elements() (in module cobra.flux_analysis.phenotype_phase_plane)
reaction_weight() (in module cobra.flux_analysis.phenotype_phase_plane)
reactions (cobra.core.model.Model attribute)
(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)
reduced_cost (cobra.core.reaction.Reaction attribute)
reduced_costs (cobra.core.solution.Solution attribute)
remove() (cobra.core.dictlist.DictList method)
remove_cons_vars() (cobra.core.model.Model method)
remove_cons_vars_from_problem() (in module cobra.util.solver)
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_metabolites() (cobra.core.model.Model method)
remove_reactions() (cobra.core.model.Model method)
rename_genes() (in module cobra.manipulation.modify)
repair() (cobra.core.model.Model method)
reset() (cobra.util.context.HistoryManager method)
resettable() (in module cobra.util.context)
rev_idx (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
reverse() (cobra.core.dictlist.DictList method)
reverse_id (cobra.core.reaction.Reaction attribute)
reverse_variable (cobra.core.reaction.Reaction attribute)
reversibility (cobra.core.reaction.Reaction attribute)
revert_to_reversible() (in module cobra.manipulation.modify)
S
sample() (cobra.flux_analysis.sampling.ACHRSampler method)
(cobra.flux_analysis.sampling.HRSampler method)
(cobra.flux_analysis.sampling.OptGPSampler method)
(in module cobra.flux_analysis.sampling)
save_json_model() (in module cobra.io.json)
save_matlab_model() (in module cobra.io.mat)
seed (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
segment() (cobra.flux_analysis.phenotype_phase_plane.phenotypePhasePlaneData method)
separate_forward_and_reverse_bounds() (in module cobra.core.reaction)
set_attrib() (in module cobra.io.sbml3)
set_objective() (in module cobra.util.solver)
set_up_optknock() (in module cobra.design.design_algorithms)
shadow_price (cobra.core.metabolite.Metabolite attribute)
shadow_prices (cobra.core.solution.Solution attribute)
shared_np_array() (in module cobra.flux_analysis.sampling)
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)
slim_optimize() (cobra.core.model.Model method)
SMILEY() (in module cobra.flux_analysis.gapfilling)
Solution (class in cobra.core.solution)
solution (cobra.core.model.Model attribute)
solve_moma_model() (in module cobra.flux_analysis.moma)
solver (cobra.core.model.Model attribute)
(cobra.core.solution.LegacySolution attribute)
SolverNotFound
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)
status (cobra.core.solution.Solution attribute)
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)
T
terminate() (cobra.flux_analysis.deletion_worker.CobraDeletionMockPool method)
(cobra.flux_analysis.deletion_worker.CobraDeletionPool method)
thinning (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
to_array_based_model() (cobra.core.model.Model method)
to_frame() (cobra.core.solution.Solution method)
to_json() (in module cobra.io.json)
total_components_flux() (in module cobra.flux_analysis.phenotype_phase_plane)
total_yield() (in module cobra.flux_analysis.phenotype_phase_plane)
U
Unbounded
UndefinedSolution
undelete_model_genes() (in module cobra.manipulation.delete)
union() (cobra.core.dictlist.DictList method)
update_costs() (cobra.flux_analysis.gapfilling.GapFiller method)
update_forward_and_reverse_bounds() (in module cobra.core.reaction)
upper_bound (cobra.core.reaction.Reaction attribute)
V
validate() (cobra.flux_analysis.gapfilling.GapFiller method)
(cobra.flux_analysis.sampling.HRSampler method)
validate_sbml_model() (in module cobra.io.sbml3)
variable_bounds (cobra.flux_analysis.sampling.Problem attribute)
,
[1]
variable_fixed (cobra.flux_analysis.sampling.Problem attribute)
variables (cobra.core.model.Model attribute)
visit_BinOp() (cobra.core.gene.GPRCleaner method)
visit_Name() (cobra.core.gene.GPRCleaner method)
W
warmup (cobra.flux_analysis.sampling.ACHRSampler attribute)
(cobra.flux_analysis.sampling.HRSampler attribute)
(cobra.flux_analysis.sampling.OptGPSampler attribute)
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)
(cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
,
[1]
x_dict (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
,
[1]
Y
y (cobra.core.metabolite.Metabolite attribute)
(cobra.core.reaction.Reaction attribute)
(cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
,
[1]
y_dict (cobra.core.solution.LegacySolution attribute)
(cobra.core.solution.Solution attribute)
,
[1]
yield_upper_tria_indexes() (in module cobra.flux_analysis.double_deletion)
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