Index

A

add_annotation() (pysb.core.Model method) add_component() (pysb.core.Model method) add_initial() (pysb.core.SelfExporter static method) add_species() (pysb.pattern.SpeciesPatternMatcher method) all_component_sets() (pysb.core.Model method) all_components() (pysb.core.Model method)

AllObservablesInRules (class in pysb.testing.modeltests) ANY (class in pysb.core) as_complex_pattern() (in module pysb.core) as_reaction_pattern() (in module pysb.core) assemble_chain_sequential_base() (in module pysb.macros) assemble_pore_sequential() (in module pysb.macros)

B

bind() (in module pysb.macros) bind_complex() (in module pysb.macros) bind_table() (in module pysb.macros)

bind_table_complex() (in module pysb.macros) BnglExporter (class in pysb.export.bngl) build_rule_expression() (in module pysb.core)

C

catalyze() (in module pysb.macros) catalyze_complex() (in module pysb.macros) catalyze_one_step() (in module pysb.macros) catalyze_one_step_reversible() (in module pysb.macros) catalyze_state() (in module pysb.macros) check() (pysb.testing.modeltests.TestSuite method) check_all() (pysb.testing.modeltests.TestSuite method) check_dangling_bonds() (in module pysb.pattern) cleanup() (pysb.core.SelfExporter static method) Compartment (class in pysb.core)

CompartmentAlreadySpecifiedError CompartmentsNotSupported ComplexPattern (class in pysb.core) Component (class in pysb.core) ComponentDuplicateNameError ComponentSet (class in pysb.core) ConstantExpressionError contact_map (pysb.kappa.StaticAnalysisResult attribute) contact_map() (in module pysb.kappa) copy() (pysb.core.ComplexPattern method)

D

DanglingBondError degrade() (in module pysb.macros) docstring (pysb.export.Exporter attribute)

drug_binding() (in module pysb.macros) DuplicateMonomerError DuplicateSiteError

E

enable_synth_deg() (pysb.core.Model method) equilibrate() (in module pysb.macros) expand_expr() (pysb.core.Expression method) expand_obs() (pysb.core.Observable method) export() (in module pysb.export) (pysb.core.SelfExporter static method) (pysb.export.Exporter method) (pysb.export.bngl.BnglExporter method) (pysb.export.kappa.KappaExporter method) (pysb.export.pysb_flat.PysbFlatExporter method)

Exporter (class in pysb.export) ExportError Expression (class in pysb.core) ExpressionError expressions_constant() (pysb.core.Model method) expressions_dynamic() (pysb.core.Model method) ExpressionsNotSupported extract_site_conditions() (in module pysb.core)

F

filter() (pysb.core.ComponentSet method) FilterPredicate (class in pysb.pattern)

flux_map (pysb.kappa.SimulationResult attribute) Function (class in pysb.pattern)

G

get() (pysb.core.ComponentSet method) get_annotations() (pysb.core.Model method)

get_bonds_in_pattern() (in module pysb.pattern) get_half_bonds_in_pattern() (in module pysb.pattern) get_species_index() (pysb.core.Model method)

H

has_synth_deg() (pysb.core.Model method)

I

index() (pysb.core.ComponentSet method) influence_map (pysb.kappa.StaticAnalysisResult attribute) influence_map() (in module pysb.kappa) Initial (class in pysb.core) initial() (pysb.core.Model method) InitialConditionsView (class in pysb.core) InvalidComplexPatternException InvalidComponentNameError InvalidInitialConditionError InvalidReactionPatternException

InvalidReversibleSynthesisDegradationRule is_concrete() (pysb.core.ComplexPattern method) (pysb.core.MonomerPattern method) is_constant_expression() (pysb.core.Expression method) is_deg() (pysb.core.Rule method) is_equivalent_to() (pysb.core.ComplexPattern method) is_site_concrete() (pysb.core.MonomerPattern method) is_state_bond_tuple() (in module pysb.core) is_synth() (pysb.core.Rule method) items() (pysb.core.ComponentSet method)

K

KappaExporter (class in pysb.export.kappa) KasaInterfaceError

KasimInterfaceError keys() (pysb.core.ComponentSet method)

L

LocalFunctionsNotSupported

M

match() (pysb.pattern.SpeciesPatternMatcher method) match_complex_pattern() (in module pysb.pattern) match_reaction_pattern() (in module pysb.pattern) matches() (pysb.core.ComplexPattern method) (pysb.core.ReactionPattern method) MatchOnce() (in module pysb.core) Model (class in pysb.core) model (pysb.export.Exporter attribute) ModelAssertion (class in pysb.testing.modeltests)

ModelAssertionFailure ModelExistsWarning ModelNotDefinedError Module (class in pysb.pattern) modules (pysb.core.Model attribute) Monomer (class in pysb.core) MonomerPattern (class in pysb.core) monomers_from_pattern() (in module pysb.pattern) MultiState (class in pysb.core)

N

Name (class in pysb.pattern)

O

Observable (class in pysb.core)

odes (pysb.core.Model attribute) OdeView (class in pysb.core)

P

pad() (in module pysb.export) Parameter (class in pysb.core) parameters_compartments() (pysb.core.Model method) parameters_expressions() (pysb.core.Model method) parameters_initial_conditions() (pysb.core.Model method) parameters_rules() (pysb.core.Model method) parameters_unused() (pysb.core.Model method) Pattern (class in pysb.pattern) pore_bind() (in module pysb.macros) pore_transport() (in module pysb.macros)

pysb.core (module) pysb.export (module) pysb.export.bngl (module) pysb.export.kappa (module) pysb.export.pysb_flat (module) pysb.kappa (module) pysb.macros (module) pysb.pattern (module) pysb.testing.modeltests (module) PysbFlatExporter (class in pysb.export.pysb_flat)

R

ReactionAssertion (class in pysb.testing.modeltests) ReactionNetworkAssertion (class in pysb.testing.modeltests) ReactionPattern (class in pysb.core) ReactionPatternMatcher (class in pysb.pattern) RedundantSiteConditionsError reload() (pysb.core.Model method) rename() (pysb.core.Component method) (pysb.core.ComponentSet method) (pysb.core.SelfExporter static method)

reset_equations() (pysb.core.Model method) ReusedBondError Rule (class in pysb.core) rule_firing_species() (pysb.pattern.SpeciesPatternMatcher method) RuleAssertion (class in pysb.testing.modeltests) RuleExpression (class in pysb.core) RulePatternMatcher (class in pysb.pattern) run_simulation() (in module pysb.kappa) run_static_analysis() (in module pysb.kappa)

S

SelfExporter (class in pysb.core) set_kappa_path() (in module pysb.kappa) SimulationResult (class in pysb.kappa) species_fired_by_reactant_pattern() (pysb.pattern.SpeciesPatternMatcher method) SpeciesAssertion (class in pysb.testing.modeltests) SpeciesDoesNotExist (class in pysb.testing.modeltests) SpeciesExists (class in pysb.testing.modeltests) SpeciesIsProduct (class in pysb.testing.modeltests) SpeciesIsReactant (class in pysb.testing.modeltests)

SpeciesNeverProduct (class in pysb.testing.modeltests) SpeciesNeverReactant (class in pysb.testing.modeltests) SpeciesOnlyProduct (class in pysb.testing.modeltests) SpeciesOnlyReactant (class in pysb.testing.modeltests) SpeciesPatternMatcher (class in pysb.pattern) StaticAnalysisResult (class in pysb.kappa) stoichiometry_matrix (pysb.core.Model attribute) SymbolExistsWarning synthesize() (in module pysb.macros) synthesize_degrade_table() (in module pysb.macros)

T

Tag (class in pysb.core) TagAlreadySpecifiedError

TestSuite (class in pysb.testing.modeltests) timecourse (pysb.kappa.SimulationResult attribute)

U

UnknownSiteError

update_initial_condition_pattern() (pysb.core.Model method)

V

validate_const_expr() (in module pysb.core)

validate_expr() (in module pysb.core) values() (pysb.core.ComponentSet method)

W

WILD (class in pysb.core)