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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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)
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