Index

A

action() (pysb.bng.BngBaseInterface method) (pysb.bng.BngConsole method) add_annotation() (pysb.core.Model method) add_component() (pysb.core.Model method) all_component_sets() (pysb.core.Model method) all_components() (pysb.core.Model method)

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 attribute) 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 attribute)

BngBaseInterface (class in pysb.bng) BngConsole (class in pysb.bng) BngInterfaceError BnglExporter (class in pysb.export.bngl) BngNetExporter (class in pysb.export.bng_net) 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) cleanup() (pysb.core.SelfExporter static method) Compartment (class in pysb.core) 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

degrade() (in module pysb.macros)

docstring (pysb.export.Exporter attribute)

E

enable_synth_deg() (pysb.core.Model method) equilibrate() (in module pysb.macros) expand_expr() (pysb.core.Expression method) export() (in module pysb.export) (pysb.core.SelfExporter static method) (pysb.export.Exporter method) (pysb.export.bng_net.BngNetExporter method) (pysb.export.bngl.BnglExporter method) (pysb.export.kappa.KappaExporter method) (pysb.export.mathematica.MathematicaExporter method) (pysb.export.matlab.MatlabExporter method) (pysb.export.potterswheel.PottersWheelExporter method) (pysb.export.python.PythonExporter method) (pysb.export.sbml.SbmlExporter method) Exporter (class in pysb.export)

Expression (class in pysb.core) ExpressionError expressions_constant() (pysb.core.Model method) expressions_dynamic() (pysb.core.Model method) extract_site_conditions() (in module pysb.core)

F

flux_map (pysb.kappa.SimulationResult attribute)

G

generate_equations() (in module pysb.bng) generate_network() (in module pysb.bng) (pysb.bng.BngConsole method)

get_annotations() (pysb.core.Model method) get_species_index() (pysb.core.Model method)

H

has_synth_deg() (pysb.core.Model method)

I

indent() (in module pysb.export.sbml) influence_map (pysb.kappa.StaticAnalysisResult attribute) influence_map() (in module pysb.kappa) Initial() (in module pysb.core) initial() (pysb.core.Model method) 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_synth() (pysb.core.Rule method)

K

KappaExporter (class in pysb.export.kappa)

M

MatchOnce() (in module pysb.core) MathematicaExporter (class in pysb.export.mathematica) MatlabExporter (class in pysb.export.matlab) Model (class in pysb.core)

model (pysb.bng.BngBaseInterface attribute) (pysb.export.Exporter attribute) ModelExistsWarning Monomer (class in pysb.core) MonomerPattern (class in pysb.core)

N

net_filename (pysb.bng.BngBaseInterface attribute) NoInitialConditionsError

NoRulesError

O

Observable (class in pysb.core)

odesolve() (in module pysb.integrate)

P

pad() (in module pysb.export) Parameter (class in pysb.core) parameters_compartments() (pysb.core.Model method) parameters_initial_conditions() (pysb.core.Model method) parameters_rules() (pysb.core.Model method) parameters_unused() (pysb.core.Model method) 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.kappa (module) pysb.export.mathematica (module) pysb.export.matlab (module) pysb.export.potterswheel (module) pysb.export.python (module) pysb.export.sbml (module) pysb.integrate (module) pysb.kappa (module) pysb.macros (module) pysb.tools.render_reactions (module) pysb.tools.render_species (module) PythonExporter (class in pysb.export.python)

R

ReactionPattern (class in pysb.core) read_netfile() (pysb.bng.BngBaseInterface method) read_simulation_results() (pysb.bng.BngBaseInterface 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)

Rule (class in pysb.core) RuleExpression (class in pysb.core) run() (in module pysb.tools.render_reactions) (in module pysb.tools.render_species) (pysb.integrate.Solver method) run_simulation() (in module pysb.kappa) run_ssa() (in module pysb.bng) run_static_analysis() (in module pysb.kappa)

S

SbmlExporter (class in pysb.export.sbml) SelfExporter (class in pysb.core) set_kappa_path() (in module pysb.kappa) setup_module() (in module pysb.integrate) SimulationResult (class in pysb.kappa)

Solver (class in pysb.integrate) StaticAnalysisResult (class in pysb.kappa) SymbolExistsWarning synthesize() (in module pysb.macros) synthesize_degrade_table() (in module pysb.macros)

T

timecourse (pysb.kappa.SimulationResult attribute)

U

update_initial_condition_pattern() (pysb.core.Model method)

V

validate_const_expr() (in module pysb.core)

validate_expr() (in module pysb.core)

W

WILD (class in pysb.core)