PySB Modules Reference¶
- PySB core (
pysb.core
)ANY
Compartment
CompartmentAlreadySpecifiedError
ComplexPattern
Component
ComponentDuplicateNameError
ComponentSet
ConstantExpressionError
DanglingBondError
DuplicateMonomerError
DuplicateSiteError
EnergyPattern
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
MultiState
Observable
OdeView
Parameter
ReactionPattern
RedundantSiteConditionsError
ReusedBondError
Rule
RuleExpression
SelfExporter
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
) - Simulation tools (
pysb.simulator
) - Set/get paths for external tools (
pysb.pathfinder
) - Testing PySB Models (
pysb.testing.modeltests
) - BioNetGen integration (
pysb.bng
) - Kappa integration (
pysb.kappa
) - 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
) - Visualizing model structure
- Sensitivity anaylsis (
pysb.tools.sensitivity_analysis
) - Importing from other formats (
pysb.importers
) - 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
)
- Export SBML (
CompartmentsNotSupported
CustomSympyFunctionsNotSupported
EnergyNotSupported
ExportError
Exporter
ExpressionsNotSupported
FeatureNotSupportedError
LocalFunctionsNotSupported
export()
pad()