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A
ABSOLUTE_BOUNDS (cobamp.nullspace.subset_reduction.SubsetReducer attribute)
AbstractConstraint (class in cobamp.algorithms.kshortest)
AbstractObjectReader (class in cobamp.wrappers.external_wrappers)
add_c_variable() (cobamp.core.linear_systems.KShortestCompatibleLinearSystem method)
add_columns_to_model() (cobamp.core.linear_systems.LinearSystem method)
add_combinatorial_benders_cut() (cobamp.core.linear_systems.BendersMasterSystem method)
add_if_not_none() (cobamp.utilities.property_management.PropertyDictionary method)
add_metabolite() (cobamp.core.models.ConstraintBasedModel method)
add_new_properties() (cobamp.utilities.property_management.PropertyDictionary method)
add_reaction() (cobamp.core.models.ConstraintBasedModel method)
add_rows_to_model() (cobamp.core.linear_systems.LinearSystem method)
add_variables_to_model() (cobamp.core.linear_systems.LinearSystem method)
ALGORITHM_TYPE_ITERATIVE (cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper attribute)
ALGORITHM_TYPE_POPULATE (cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper attribute)
annotate_heatmap() (in module cobamp.analysis.plotting)
apply_fx_to_all_node_values() (in module cobamp.analysis.graph)
attribute_names() (cobamp.core.optimization.Solution method)
attribute_value() (cobamp.core.optimization.Solution method)
B
bak_irrev() (in module cobamp.core.linear_systems)
batch_optimize() (cobamp.core.optimization.BatchOptimizer method)
BatchOptimizer (class in cobamp.core.optimization)
BendersDecompositionOptimizer (class in cobamp.core.optimization)
BendersMasterSystem (class in cobamp.core.linear_systems)
BendersSlaveOptimizer (class in cobamp.core.optimization)
BendersSlaveSystem (class in cobamp.core.linear_systems)
boolean_precedence() (in module cobamp.utilities.postfix_expressions)
build_problem() (cobamp.core.linear_systems.BendersMasterSystem method)
(cobamp.core.linear_systems.GenericLinearSystem method)
(cobamp.core.linear_systems.IrreversibleLinearPatternSystem method)
(cobamp.core.linear_systems.LinearSystem method)
C
c (cobamp.core.linear_systems.KShortestCompatibleLinearSystem attribute)
cobamp (module)
,
[1]
cobamp.algorithms (module)
cobamp.algorithms.kshortest (module)
cobamp.analysis (module)
cobamp.analysis.frequency (module)
cobamp.analysis.graph (module)
cobamp.analysis.plotting (module)
cobamp.core (module)
cobamp.core.linear_systems (module)
cobamp.core.models (module)
cobamp.core.optimization (module)
cobamp.core.transformer (module)
cobamp.nullspace (module)
cobamp.nullspace.nullspace (module)
cobamp.nullspace.subset_reduction (module)
cobamp.utilities (module)
cobamp.utilities.file_utils (module)
cobamp.utilities.postfix_expressions (module)
cobamp.utilities.property_management (module)
cobamp.utilities.set_utils (module)
cobamp.utilities.test_utils (module)
cobamp.wrappers (module)
cobamp.wrappers.external_wrappers (module)
cobamp.wrappers.method_wrappers (module)
CobampModelObjectReader (class in cobamp.wrappers.external_wrappers)
COBRAModelObjectReader (class in cobamp.wrappers.external_wrappers)
compress_linear_paths() (in module cobamp.analysis.graph)
compute_nullspace() (in module cobamp.nullspace.nullspace)
ConstraintBasedModel (class in cobamp.core.models)
convert_constraint_ids() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
convert_gprs_to_list() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.FramedModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
CORSOModel (class in cobamp.core.models)
CORSOSolution (class in cobamp.core.optimization)
D
decode_index() (cobamp.core.models.ConstraintBasedModel method)
decode_k_shortest_solution() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
decompose_list() (in module cobamp.algorithms.kshortest)
DefaultFluxbound (class in cobamp.algorithms.kshortest)
DefaultYieldbound (class in cobamp.algorithms.kshortest)
display_heatmap() (in module cobamp.analysis.plotting)
DualLinearSystem (class in cobamp.core.linear_systems)
dummy_variable() (cobamp.core.linear_systems.LinearSystem method)
dvar_mapping (cobamp.core.linear_systems.KShortestCompatibleLinearSystem attribute)
dvars (cobamp.core.linear_systems.KShortestCompatibleLinearSystem attribute)
E
empty_constraint() (cobamp.core.linear_systems.LinearSystem method)
enumerate() (cobamp.algorithms.kshortest.KShortestEFMAlgorithm method)
ENUMERATION_METHOD_ITERATE (cobamp.algorithms.kshortest.KShortestEnumerator attribute)
ENUMERATION_METHOD_POPULATE (cobamp.algorithms.kshortest.KShortestEnumerator attribute)
eval_boolean_operator() (in module cobamp.utilities.postfix_expressions)
eval_math_operator() (in module cobamp.utilities.postfix_expressions)
evaluate_postfix_expression() (in module cobamp.utilities.postfix_expressions)
exclude_solutions() (cobamp.algorithms.kshortest.KShortestEnumerator method)
F
find_all_tree_nodes() (in module cobamp.analysis.graph)
fix_backwards_irreversible_reactions() (in module cobamp.core.linear_systems)
flux_limits() (cobamp.core.models.ConstraintBasedModel method)
force_solutions() (cobamp.algorithms.kshortest.KShortestEnumerator method)
FramedModelObjectReader (class in cobamp.wrappers.external_wrappers)
from_new() (cobamp.core.transformer.ReactionIndexMapping method)
from_original() (cobamp.core.transformer.ReactionIndexMapping method)
from_tuple() (cobamp.algorithms.kshortest.AbstractConstraint method)
(cobamp.algorithms.kshortest.DefaultFluxbound method)
(cobamp.algorithms.kshortest.DefaultYieldbound method)
fwd_irrev() (in module cobamp.core.linear_systems)
G
g2rx() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
generate_dual_problem() (cobamp.core.linear_systems.DualLinearSystem method)
generate_target_matrix() (cobamp.algorithms.kshortest.InterventionProblem method)
GenericLinearSystem (class in cobamp.core.linear_systems)
get_active_indicator_varids() (cobamp.core.optimization.KShortestSolution method)
get_bounds_as_list() (cobamp.core.models.ConstraintBasedModel method)
get_c_variable() (cobamp.core.linear_systems.KShortestCompatibleLinearSystem method)
get_configuration() (cobamp.core.linear_systems.LinearSystem method)
get_constraint_bounds() (cobamp.core.linear_systems.LinearSystem method)
get_constraint_matrices() (cobamp.core.linear_systems.LinearSystem method)
get_default_solver() (in module cobamp.core.linear_systems)
get_dvar_mapping() (cobamp.core.linear_systems.KShortestCompatibleLinearSystem method)
get_dvars() (cobamp.core.linear_systems.KShortestCompatibleLinearSystem method)
get_enumerator() (cobamp.algorithms.kshortest.KShortestEFMAlgorithm method)
(cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper method)
get_frequency_dataframe() (in module cobamp.analysis.frequency)
get_gene_protein_reaction_rule() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
get_irreversibilities() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.CobampModelObjectReader method)
(cobamp.wrappers.external_wrappers.FramedModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_linear_system() (cobamp.wrappers.method_wrappers.KShortestEFMEnumeratorWrapper method)
(cobamp.wrappers.method_wrappers.KShortestEFPEnumeratorWrapper method)
(cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper method)
(cobamp.wrappers.method_wrappers.KShortestMCSEnumeratorWrapper method)
get_mandatory_properties() (cobamp.utilities.property_management.PropertyDictionary method)
get_model() (cobamp.algorithms.kshortest.KShortestEnumerator method)
(cobamp.core.linear_systems.LinearSystem method)
get_model_bounds() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.CobampModelObjectReader method)
(cobamp.wrappers.external_wrappers.FramedModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_model_genes() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_model_gprs() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_optional_properties() (cobamp.utilities.property_management.PropertyDictionary method)
get_reaction_activity() (cobamp.core.optimization.GIMMESolution method)
get_reaction_and_metabolite_ids() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.CobampModelObjectReader method)
(cobamp.wrappers.external_wrappers.FramedModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_reaction_bounds() (cobamp.core.models.ConstraintBasedModel method)
get_rx_instances() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.CobampModelObjectReader method)
(cobamp.wrappers.external_wrappers.FramedModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_single_solution() (cobamp.algorithms.kshortest.KShortestEnumerator method)
get_solver_interfaces() (in module cobamp.core.linear_systems)
get_stoich_matrix_shape() (cobamp.core.linear_systems.LinearSystem method)
get_stoichiometric_matrix() (cobamp.core.models.ConstraintBasedModel method)
(cobamp.wrappers.external_wrappers.AbstractObjectReader method)
(cobamp.wrappers.external_wrappers.COBRAModelObjectReader method)
(cobamp.wrappers.external_wrappers.CobampModelObjectReader method)
(cobamp.wrappers.external_wrappers.FramedModelObjectReader method)
(cobamp.wrappers.external_wrappers.MatFormatReader method)
get_stuff() (cobamp.core.linear_systems.LinearSystem method)
get_system_matrix() (cobamp.core.linear_systems.LinearSystem method)
get_transform_maps() (cobamp.nullspace.subset_reduction.SubsetReducer method)
get_working_gene_names() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
GIMMEModel (class in cobamp.core.models)
GIMMESolution (class in cobamp.core.optimization)
H
has_no_overlap() (in module cobamp.utilities.set_utils)
has_required_properties() (cobamp.utilities.property_management.PropertyDictionary method)
heatmap() (in module cobamp.analysis.plotting)
I
ignore_compressed_nodes_by_size() (in module cobamp.analysis.graph)
initialize_optimizer() (cobamp.core.models.ConstraintBasedModel method)
InterventionProblem (class in cobamp.algorithms.kshortest)
IrreversibleLinearPatternSystem (class in cobamp.core.linear_systems)
IrreversibleLinearSystem (class in cobamp.core.linear_systems)
is_boolean_operator() (in module cobamp.utilities.postfix_expressions)
is_boolean_value() (in module cobamp.utilities.postfix_expressions)
is_identical() (in module cobamp.utilities.set_utils)
is_number_token() (in module cobamp.utilities.postfix_expressions)
is_operator_token() (in module cobamp.utilities.postfix_expressions)
is_reversible_reaction() (cobamp.core.models.ConstraintBasedModel method)
is_string_token() (in module cobamp.utilities.postfix_expressions)
is_subset() (in module cobamp.utilities.set_utils)
K
KShortestCompatibleLinearSystem (class in cobamp.core.linear_systems)
KShortestEFMAlgorithm (class in cobamp.algorithms.kshortest)
KShortestEFMEnumeratorWrapper (class in cobamp.wrappers.method_wrappers)
KShortestEFPEnumeratorWrapper (class in cobamp.wrappers.method_wrappers)
KShortestEnumerator (class in cobamp.algorithms.kshortest)
KShortestEnumeratorWrapper (class in cobamp.wrappers.method_wrappers)
KShortestMCSEnumeratorWrapper (class in cobamp.wrappers.method_wrappers)
KShortestProperties (class in cobamp.algorithms.kshortest)
KShortestSolution (class in cobamp.core.optimization)
L
left_operator_association() (in module cobamp.utilities.postfix_expressions)
LinearSystem (class in cobamp.core.linear_systems)
LinearSystemOptimizer (class in cobamp.core.optimization)
M
make_irreversible() (cobamp.core.models.ConstraintBasedModel method)
make_irreversible_model() (in module cobamp.core.linear_systems)
make_irreversible_model_raven() (in module cobamp.core.models)
materialize() (cobamp.algorithms.kshortest.AbstractConstraint method)
(cobamp.algorithms.kshortest.DefaultFluxbound method)
(cobamp.algorithms.kshortest.DefaultYieldbound method)
MatFormatReader (class in cobamp.wrappers.external_wrappers)
merge_duplicate_nodes() (in module cobamp.analysis.graph)
metabolite_id_to_index() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
model (cobamp.core.linear_systems.LinearSystem attribute)
ModelTransformer (class in cobamp.core.transformer)
multiply() (cobamp.core.transformer.ReactionIndexMapping method)
N
normalize_boolean_expression() (in module cobamp.wrappers.external_wrappers)
nullspace_blocked_reactions() (in module cobamp.nullspace.nullspace)
O
objective_value() (cobamp.core.optimization.Solution method)
op_prec() (in module cobamp.utilities.postfix_expressions)
open_file() (in module cobamp.utilities.file_utils)
optimization_pool() (in module cobamp.core.optimization)
optimize() (cobamp.core.models.ConstraintBasedModel method)
(cobamp.core.optimization.BendersDecompositionOptimizer method)
(cobamp.core.optimization.BendersSlaveOptimizer method)
(cobamp.core.optimization.LinearSystemOptimizer method)
optimize_corso() (cobamp.core.models.CORSOModel method)
optimize_gimme() (cobamp.core.models.GIMMEModel method)
P
parametrize() (cobamp.core.linear_systems.BendersSlaveSystem method)
parse_infix_expression() (in module cobamp.utilities.postfix_expressions)
pickle_object() (in module cobamp.utilities.file_utils)
populate() (cobamp.core.optimization.LinearSystemOptimizer method)
populate_constraints_from_matrix() (cobamp.core.linear_systems.LinearSystem method)
populate_current_size() (cobamp.algorithms.kshortest.KShortestEnumerator method)
populate_model_from_matrix() (cobamp.core.linear_systems.LinearSystem method)
populate_nx_graph() (in module cobamp.analysis.graph)
population_iterator() (cobamp.algorithms.kshortest.KShortestEnumerator method)
prepare_irreversible_system() (in module cobamp.core.linear_systems)
pretty_print_tree() (in module cobamp.analysis.graph)
probabilistic_tree_compression() (in module cobamp.analysis.graph)
probabilistic_tree_prune() (in module cobamp.analysis.graph)
PropertyDictionary (class in cobamp.utilities.property_management)
push() (cobamp.utilities.postfix_expressions.Queue method)
(cobamp.utilities.postfix_expressions.Stack method)
Q
Queue (class in cobamp.utilities.postfix_expressions)
R
random_string_generator() (in module cobamp.core.optimization)
reaction_id_to_index() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
ReactionIndexMapping (class in cobamp.core.transformer)
read_pickle() (in module cobamp.utilities.file_utils)
reduce() (cobamp.nullspace.subset_reduction.SubsetReducer method)
(in module cobamp.nullspace.subset_reduction)
remove_cuts() (cobamp.core.linear_systems.BendersMasterSystem method)
remove_from_model() (cobamp.core.linear_systems.LinearSystem method)
remove_metabolite() (cobamp.core.models.ConstraintBasedModel method)
remove_reaction() (cobamp.core.models.ConstraintBasedModel method)
reset_enumerator_state() (cobamp.algorithms.kshortest.KShortestEnumerator method)
revert_to_original_bounds() (cobamp.core.models.ConstraintBasedModel method)
S
select_solver() (cobamp.core.linear_systems.LinearSystem method)
set_attribute() (cobamp.core.optimization.Solution method)
set_constraint_bounds() (cobamp.core.linear_systems.LinearSystem method)
set_corso_objective() (cobamp.core.models.CORSOModel method)
set_costs() (cobamp.core.models.CORSOModel method)
set_default_configuration() (cobamp.core.linear_systems.LinearSystem method)
set_indicator_activity() (cobamp.algorithms.kshortest.KShortestEnumerator method)
set_number_of_threads() (cobamp.core.linear_systems.LinearSystem method)
set_objective() (cobamp.core.linear_systems.LinearSystem method)
(cobamp.core.models.ConstraintBasedModel method)
set_objective_expression() (cobamp.algorithms.kshortest.KShortestEnumerator method)
set_reaction_bounds() (cobamp.core.models.ConstraintBasedModel method)
set_size_constraint() (cobamp.algorithms.kshortest.KShortestEnumerator method)
set_stoichiometric_matrix() (cobamp.core.models.ConstraintBasedModel method)
set_variable_bounds() (cobamp.core.linear_systems.LinearSystem method)
set_variable_types() (cobamp.core.linear_systems.LinearSystem method)
set_working_memory_limit() (cobamp.core.linear_systems.LinearSystem method)
SIGNED_INDICATOR_SUM (cobamp.core.optimization.KShortestSolution attribute)
SIGNED_VALUE_MAP (cobamp.core.optimization.KShortestSolution attribute)
Solution (class in cobamp.core.optimization)
solution_iterator() (cobamp.algorithms.kshortest.KShortestEnumerator method)
solve_original_model() (cobamp.core.models.CORSOModel method)
Stack (class in cobamp.utilities.postfix_expressions)
status() (cobamp.core.optimization.Solution method)
SteadyStateLinearSystem (class in cobamp.core.linear_systems)
subset_candidates() (in module cobamp.nullspace.subset_reduction)
subset_correlation_matrix() (in module cobamp.nullspace.subset_reduction)
subset_reduction() (in module cobamp.nullspace.subset_reduction)
SubsetReducer (class in cobamp.nullspace.subset_reduction)
SubsetReducerProperties (class in cobamp.nullspace.subset_reduction)
T
timeit() (in module cobamp.utilities.test_utils)
TO_BLOCK (cobamp.nullspace.subset_reduction.SubsetReducer attribute)
to_cobamp_cbm() (cobamp.wrappers.external_wrappers.AbstractObjectReader method)
TO_KEEP_SINGLE (cobamp.nullspace.subset_reduction.SubsetReducer attribute)
to_series() (cobamp.core.optimization.Solution method)
tokenize_boolean_expression() (in module cobamp.utilities.postfix_expressions)
tokenize_infix_expression() (in module cobamp.utilities.postfix_expressions)
top() (cobamp.utilities.postfix_expressions.Queue method)
(cobamp.utilities.postfix_expressions.Stack method)
transform() (cobamp.core.transformer.ModelTransformer method)
transform_array() (cobamp.core.transformer.ModelTransformer method)
(cobamp.nullspace.subset_reduction.SubsetReducer method)
V
value_map_apply() (in module cobamp.algorithms.kshortest)
var_values() (cobamp.core.optimization.Solution method)
W
was_built() (cobamp.core.linear_systems.LinearSystem method)
write_to_lp() (cobamp.core.linear_systems.LinearSystem method)
X
x() (cobamp.core.optimization.Solution method)
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