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Index
A
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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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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_species() (pysb.pattern.SpeciesPatternMatcher method)
all (pysb.simulator.SimulationResult attribute)
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 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)
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
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)
copy() (pysb.core.ComplexPattern method)
CupSodaSimulator (class in pysb.simulator)
D
DanglingBondError
dataframe (pysb.simulator.SimulationResult attribute)
degrade() (in module pysb.macros)
docstring (pysb.export.Exporter attribute)
DuplicateMonomerError
DuplicateSiteError
E
enable_synth_deg() (pysb.core.Model method)
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.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.pysb_flat.PysbFlatExporter method)
(pysb.export.python.PythonExporter 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 attribute)
expressions_constant() (pysb.core.Model method)
expressions_dynamic() (pysb.core.Model method)
ExpressionsNotSupported
extract_site_conditions() (in module pysb.core)
F
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_species_index() (pysb.core.Model method)
H
has_synth_deg() (pysb.core.Model method)
I
indent() (in module pysb.export.sbml)
index() (pysb.core.ComponentSet method)
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)
items() (pysb.core.ComponentSet method)
iteritems() (pysb.core.ComponentSet method)
iterkeys() (pysb.core.ComponentSet method)
itervalues() (pysb.core.ComponentSet method)
K
KappaExporter (class in pysb.export.kappa)
KasaInterfaceError
KasimInterfaceError
keys() (pysb.core.ComponentSet method)
L
load() (pysb.simulator.SimulationResult class method)
load_bngl() (pysb.bng.BngConsole method)
load_equations() (in module pysb.bng)
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
Module (class in pysb.pattern)
modules (pysb.core.Model attribute)
Monomer (class in pysb.core)
MonomerPattern (class in pysb.core)
monomers_from_pattern() (in module pysb.pattern)
N
Name (class in pysb.pattern)
net_filename (pysb.bng.BngBaseInterface attribute)
NoInitialConditionsError
NoRulesError
nsims (pysb.simulator.SimulationResult attribute)
O
Observable (class in pysb.core)
observable() (pysb.simulator.SimulationResult method)
observables (pysb.simulator.SimulationResult attribute)
odes (pysb.core.Model attribute)
odesolve() (in module pysb.integrate)
OdeView (class in pysb.core)
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)
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.kappa (module)
pysb.export.mathematica (module)
pysb.export.matlab (module)
pysb.export.potterswheel (module)
pysb.export.pysb_flat (module)
pysb.export.python (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.pattern (module)
pysb.simulator (module)
pysb.testing.modeltests (module)
pysb.tools.render_reactions (module)
pysb.tools.render_species (module)
PysbFlatExporter (class in pysb.export.pysb_flat)
PythonExporter (class in pysb.export.python)
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)
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)
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.ScipyOdeSimulator method)
(pysb.simulator.StochKitSimulator 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)
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)
SimulationResult (class in pysb.kappa)
(class in pysb.simulator)
Solver (class in pysb.integrate)
species (pysb.simulator.SimulationResult attribute)
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 attribute)
SymbolExistsWarning
synthesize() (in module pysb.macros)
synthesize_degrade_table() (in module pysb.macros)
T
TestSuite (class in pysb.testing.modeltests)
timecourse (pysb.kappa.SimulationResult attribute)
U
UnknownSiteError
update_initial_condition_pattern() (pysb.core.Model method)
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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