Index

A

action() (pysb.bng.BngBaseInterface method) (pysb.bng.BngConsole method) (pysb.bng.BngFileInterface method) 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 (pysb.simulator.SimulationResult property)

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

base_filename (pysb.bng.BngBaseInterface property) bind() (in module pysb.macros) bind_complex() (in module pysb.macros) bind_table() (in module pysb.macros) bind_table_complex() (in module pysb.macros) bng_filename (pysb.bng.BngBaseInterface property) BngBaseInterface (class in pysb.bng)

BngConsole (class in pysb.bng) BngFileInterface (class in pysb.bng) BngInterfaceError BnglExporter (class in pysb.export.bngl) BngNetExporter (class in pysb.export.bng_net) BngSimulator (class in pysb.simulator) build_rule_expression() (in module pysb.core)

C

cartesian_product() (in module pysb.tools.sensitivity_analysis) 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) convert() (pysb.export.sbml.SbmlExporter method) copy() (pysb.core.ComplexPattern method) create_boxplot_and_heatplot() (pysb.tools.sensitivity_analysis.PairwiseSensitivity method) create_individual_pairwise_plots() (pysb.tools.sensitivity_analysis.PairwiseSensitivity method) create_plot_p_h_pprime() (pysb.tools.sensitivity_analysis.PairwiseSensitivity method) CupSodaSimulator (class in pysb.simulator) CustomSympyFunctionsNotSupported

D

DanglingBondError dataframe (pysb.simulator.SimulationResult property) default() (pysb.export.json.PySBJSONEncoder method) 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) EnergyNotSupported EnergyPattern (class in pysb.core) equilibrate() (in module pysb.macros) execute() (pysb.bng.BngFileInterface method) expand_expr() (pysb.core.Expression method) expand_obs() (pysb.core.Observable method) export() (in module pysb.export) (pysb.core.SelfExporter static method) (pysb.export.bng_net.BngNetExporter method) (pysb.export.bngl.BnglExporter method) (pysb.export.Exporter method) (pysb.export.json.JsonExporter method) (pysb.export.kappa.KappaExporter method) (pysb.export.mathematica.MathematicaExporter method) (pysb.export.matlab.MatlabExporter method) (pysb.export.potterswheel.PottersWheelExporter method) (pysb.export.pysb_flat.PysbFlatExporter method) (pysb.export.sbml.SbmlExporter method) (pysb.export.stochkit.StochKitExporter method)

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

F

FeatureNotSupportedError filter() (pysb.core.ComponentSet method)

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

G

generate_equations() (in module pysb.bng) generate_network() (in module pysb.bng) (pysb.bng.BngConsole method) 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_path() (in module pysb.pathfinder) 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) InitialsSensitivity (class in pysb.tools.sensitivity_analysis) 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)

J

JsonExporter (class in pysb.export.json)

K

KappaExporter (class in pysb.export.kappa) KappaSimulator (class in pysb.simulator)

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

L

list_programs() (in module pysb.pathfinder) load() (pysb.simulator.SimulationResult class method)

load_bngl() (pysb.bng.BngConsole method) load_equations() (in module pysb.bng) 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) MathematicaExporter (class in pysb.export.mathematica) MatlabExporter (class in pysb.export.matlab) Model (class in pysb.core) model (pysb.export.Exporter attribute) model_from_biomodels() (in module pysb.importers.sbml) model_from_bngl() (in module pysb.importers.bngl) model_from_sbml() (in module pysb.importers.sbml) ModelAssertion (class in pysb.testing.modeltests) ModelAssertionFailure ModelExistsWarning ModelNotDefinedError module pysb.bng pysb.core pysb.export pysb.export.bng_net pysb.export.bngl pysb.export.json pysb.export.kappa pysb.export.mathematica pysb.export.matlab pysb.export.potterswheel pysb.export.pysb_flat pysb.export.sbml pysb.export.stochkit pysb.importers.bngl pysb.importers.sbml pysb.integrate pysb.kappa pysb.macros pysb.pathfinder pysb.pattern pysb.simulator pysb.testing.modeltests pysb.tools.render_reactions pysb.tools.render_species pysb.tools.sensitivity_analysis

Module (class in pysb.pattern) modules (pysb.core.Model property) 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) net_filename (pysb.bng.BngBaseInterface property)

NoInitialConditionsError NoRulesError nsims (pysb.simulator.SimulationResult property)

O

Observable (class in pysb.core) observable() (pysb.simulator.SimulationResult method) observables (pysb.simulator.SimulationResult property)

odes (pysb.core.Model property) odesolve() (in module pysb.integrate) OdeView (class in pysb.core)

P

pad() (in module pysb.export) PairwiseSensitivity (class in pysb.tools.sensitivity_analysis) Parameter (class in pysb.core) parameters_all() (pysb.core.Model method) 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) parse_bngl_expr() (in module pysb.bng) Pattern (class in pysb.pattern) PopulationMap (class in pysb.simulator) pore_bind() (in module pysb.macros) pore_transport() (in module pysb.macros) PottersWheelExporter (class in pysb.export.potterswheel) pysb.bng module pysb.core module pysb.export module pysb.export.bng_net module pysb.export.bngl module pysb.export.json module pysb.export.kappa module pysb.export.mathematica module pysb.export.matlab module pysb.export.potterswheel module

pysb.export.pysb_flat module pysb.export.sbml module pysb.export.stochkit module pysb.importers.bngl module pysb.importers.sbml module pysb.integrate module pysb.kappa module pysb.macros module pysb.pathfinder module pysb.pattern module pysb.simulator module pysb.testing.modeltests module pysb.tools.render_reactions module pysb.tools.render_species module pysb.tools.sensitivity_analysis module PysbFlatExporter (class in pysb.export.pysb_flat) PySBJSONEncoder (class in pysb.export.json) PySBJSONWithNetworkEncoder (class in pysb.export.json)

R

ReactionAssertion (class in pysb.testing.modeltests) ReactionNetworkAssertion (class in pysb.testing.modeltests) ReactionPattern (class in pysb.core) ReactionPatternMatcher (class in pysb.pattern) read_netfile() (pysb.bng.BngBaseInterface method) read_simulation_results() (pysb.bng.BngBaseInterface method) read_simulation_results_multi() (pysb.bng.BngBaseInterface static method) 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) rules_energy() (pysb.core.Model method) run() (in module pysb.tools.render_reactions) (in module pysb.tools.render_species) (pysb.integrate.Solver method) (pysb.simulator.BngSimulator method) (pysb.simulator.CupSodaSimulator method) (pysb.simulator.KappaSimulator method) (pysb.simulator.ScipyOdeSimulator method) (pysb.simulator.StochKitSimulator method) (pysb.tools.sensitivity_analysis.PairwiseSensitivity method) run_simulation() (in module pysb.kappa) run_ssa() (in module pysb.bng) run_static_analysis() (in module pysb.kappa)

S

save() (pysb.simulator.SimulationResult method) sbml_translator() (in module pysb.importers.sbml) SbmlExporter (class in pysb.export.sbml) ScipyOdeSimulator (class in pysb.simulator) SelfExporter (class in pysb.core) sensitivity_multiset (pysb.tools.sensitivity_analysis.PairwiseSensitivity property) set_bng_path() (in module pysb.bng) set_concentration() (pysb.bng.BngFileInterface method) set_kappa_path() (in module pysb.kappa) set_parameter() (pysb.bng.BngFileInterface method) set_path() (in module pysb.pathfinder) SimulationResult (class in pysb.kappa) (class in pysb.simulator) Solver (class in pysb.integrate) species (pysb.simulator.SimulationResult property) 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) StochKitExporter (class in pysb.export.stochkit) StochKitSimulator (class in pysb.simulator) stoichiometry_matrix (pysb.core.Model property) 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) uses_energy (pysb.core.Model property)

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)