PySB Modules Reference

• PySB core (pysb.core)
  • ANY
  • Compartment
  • CompartmentAlreadySpecifiedError
  • ComplexPattern
    • ComplexPattern.copy()
    • ComplexPattern.is_concrete()
    • ComplexPattern.is_equivalent_to()
    • ComplexPattern.matches()
  • Component
    • Component.rename()
  • ComponentDuplicateNameError
  • ComponentSet
    • ComponentSet.filter()
    • ComponentSet.get()
    • ComponentSet.index()
    • ComponentSet.items()
    • ComponentSet.keys()
    • ComponentSet.rename()
    • ComponentSet.values()
  • ConstantExpressionError
  • DanglingBondError
  • DuplicateMonomerError
  • DuplicateSiteError
  • EnergyPattern
  • Expression
    • Expression.expand_expr()
    • Expression.is_constant_expression()
  • ExpressionError
  • Initial
  • InitialConditionsView
  • InvalidComplexPatternException
  • InvalidComponentNameError
  • InvalidInitialConditionError
  • InvalidReactionPatternException
  • InvalidReversibleSynthesisDegradationRule
  • MatchOnce()
  • Model
    • Model.add_annotation()
    • Model.add_component()
    • Model.all_component_sets()
    • Model.all_components()
    • Model.enable_synth_deg()
    • Model.expressions_constant()
    • Model.expressions_dynamic()
    • Model.get_annotations()
    • Model.get_species_index()
    • Model.has_synth_deg()
    • Model.initial()
    • Model.modules
    • Model.odes
    • Model.parameters_all()
    • Model.parameters_compartments()
    • Model.parameters_expressions()
    • Model.parameters_initial_conditions()
    • Model.parameters_rules()
    • Model.parameters_unused()
    • Model.reload()
    • Model.reset_equations()
    • Model.rules_energy()
    • Model.stoichiometry_matrix
    • Model.update_initial_condition_pattern()
    • Model.uses_energy
  • ModelExistsWarning
  • ModelNotDefinedError
  • Monomer
  • MonomerPattern
    • MonomerPattern.is_concrete()
    • MonomerPattern.is_site_concrete()
  • MultiState
  • Observable
    • Observable.expand_obs()
  • OdeView
  • Parameter
  • ReactionPattern
    • ReactionPattern.matches()
  • RedundantSiteConditionsError
  • ReusedBondError
  • Rule
    • Rule.is_deg()
    • Rule.is_synth()
  • RuleExpression
  • SelfExporter
    • SelfExporter.add_initial()
    • SelfExporter.cleanup()
    • SelfExporter.export()
    • SelfExporter.rename()
  • SymbolExistsWarning
  • Tag
  • TagAlreadySpecifiedError
  • UnknownSiteError
  • WILD
  • as_complex_pattern()
  • as_reaction_pattern()
  • build_rule_expression()
  • extract_site_conditions()
  • is_state_bond_tuple()
  • validate_const_expr()
  • validate_expr()
• ODE integrators (pysb.integrate)
  • Solver
    • Solver.run()
  • odesolve()
• Simulation tools (pysb.simulator)
  • BngSimulator
    • BngSimulator.run()
  • CudaSSASimulator
    • CudaSSASimulator.run()
  • CupSodaSimulator
    • CupSodaSimulator.run()
  • KappaSimulator
    • KappaSimulator.run()
  • OpenCLSSASimulator
    • OpenCLSSASimulator.run()
  • PopulationMap
  • ScipyOdeSimulator
    • ScipyOdeSimulator.run()
  • SimulationResult
    • SimulationResult.all
    • SimulationResult.dataframe
    • SimulationResult.expressions
    • SimulationResult.load()
    • SimulationResult.nsims
    • SimulationResult.observable()
    • SimulationResult.observables
    • SimulationResult.save()
    • SimulationResult.species
  • StochKitSimulator
    • StochKitSimulator.run()
• Set/get paths for external tools (pysb.pathfinder)
  • get_path()
  • list_programs()
  • set_path()
• Testing PySB Models (pysb.testing.modeltests)
  • AllObservablesInRules
  • ModelAssertion
  • ModelAssertionFailure
  • ReactionAssertion
  • ReactionNetworkAssertion
  • RuleAssertion
  • SpeciesAssertion
  • SpeciesDoesNotExist
  • SpeciesExists
  • SpeciesIsProduct
  • SpeciesIsReactant
  • SpeciesNeverProduct
  • SpeciesNeverReactant
  • SpeciesOnlyProduct
  • SpeciesOnlyReactant
  • TestSuite
    • TestSuite.check()
    • TestSuite.check_all()
• BioNetGen integration (pysb.bng)
  • BngBaseInterface
    • BngBaseInterface.action()
    • BngBaseInterface.base_filename
    • BngBaseInterface.bng_filename
    • BngBaseInterface.net_filename
    • BngBaseInterface.read_netfile()
    • BngBaseInterface.read_simulation_results()
    • BngBaseInterface.read_simulation_results_multi()
  • BngConsole
    • BngConsole.action()
    • BngConsole.generate_network()
    • BngConsole.load_bngl()
  • BngFileInterface
    • BngFileInterface.action()
    • BngFileInterface.execute()
    • BngFileInterface.set_concentration()
    • BngFileInterface.set_parameter()
  • BngInterfaceError
  • NoInitialConditionsError
  • NoRulesError
  • generate_equations()
  • generate_network()
  • load_equations()
  • parse_bngl_expr()
  • run_ssa()
  • set_bng_path()
• Kappa integration (pysb.kappa)
  • KasaInterfaceError
  • KasimInterfaceError
  • SimulationResult
    • SimulationResult.flux_map
    • SimulationResult.timecourse
  • StaticAnalysisResult
    • StaticAnalysisResult.contact_map
    • StaticAnalysisResult.influence_map
  • contact_map()
  • influence_map()
  • run_simulation()
  • run_static_analysis()
  • set_kappa_path()
• Macros (pysb.macros)
  • assemble_chain_sequential_base()
  • assemble_pore_sequential()
  • bind()
  • bind_complex()
  • bind_table()
  • bind_table_complex()
  • catalyze()
  • catalyze_complex()
  • catalyze_one_step()
  • catalyze_one_step_reversible()
  • catalyze_state()
  • degrade()
  • drug_binding()
  • equilibrate()
  • pore_bind()
  • pore_transport()
  • synthesize()
  • synthesize_degrade_table()
• Pattern matching against PySB models (pysb.pattern)
  • FilterPredicate
  • Function
  • Module
  • Name
  • Pattern
  • ReactionPatternMatcher
  • RulePatternMatcher
  • SpeciesPatternMatcher
    • SpeciesPatternMatcher.add_species()
    • SpeciesPatternMatcher.match()
    • SpeciesPatternMatcher.rule_firing_species()
    • SpeciesPatternMatcher.species_fired_by_reactant_pattern()
  • check_dangling_bonds()
  • get_bonds_in_pattern()
  • get_half_bonds_in_pattern()
  • match_complex_pattern()
  • match_reaction_pattern()
  • monomers_from_pattern()
• Visualizing model structure
  • Render a model’s reaction network (pysb.tools.render_reactions)
    • Usage
    • Output for Robertson example model
    • run()
  • Render a model’s species (pysb.tools.render_species)
    • run()
• Sensitivity anaylsis (pysb.tools.sensitivity_analysis)
  • InitialsSensitivity
  • PairwiseSensitivity
    • PairwiseSensitivity.create_boxplot_and_heatplot()
    • PairwiseSensitivity.create_individual_pairwise_plots()
    • PairwiseSensitivity.create_plot_p_h_pprime()
    • PairwiseSensitivity.run()
    • PairwiseSensitivity.sensitivity_multiset
  • cartesian_product()
• Importing from other formats (pysb.importers)
  • model_from_bngl()
  • model_from_biomodels()
  • model_from_sbml()
  • sbml_translator()
• Exporting to other formats (pysb.export)
  • Command-line usage
  • Interactive usage
  • Implementation of specific exporters
    • Export SBML (pysb.export.sbml)
    • Export ODEs to MATLAB (pysb.export.matlab)
    • Export ODEs to Mathematica (pysb.export.mathematica)
    • Export ODEs to PottersWheel (pysb.export.potterswheel)
    • Export BNGL (pysb.export.bngl)
    • Export BNGL NET file (pysb.export.bng_net)
    • Export Kappa (pysb.export.kappa)
    • Export a “flat” PySB model (pysb.export.pysb_flat)
    • Export to StochKit (pysb.export.stochkit)
    • Export JSON (pysb.export.json)
  • CompartmentsNotSupported
  • CustomSympyFunctionsNotSupported
  • EnergyNotSupported
  • ExportError
  • Exporter
    • Exporter.docstring
    • Exporter.export()
    • Exporter.model
  • ExpressionsNotSupported
  • FeatureNotSupportedError
  • LocalFunctionsNotSupported
  • export()
  • pad()