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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
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_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
bind() (in module pysb.macros)
bind_complex() (in module pysb.macros)
bind_table() (in module pysb.macros)
bind_table_complex() (in module pysb.macros)
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)
D
DanglingBondError
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)
equilibrate() (in module pysb.macros)
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.kappa.KappaExporter method)
(pysb.export.pysb_flat.PysbFlatExporter method)
Exporter (class in pysb.export)
ExportError
Expression (class in pysb.core)
ExpressionError
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
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
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)
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)
K
KappaExporter (class in pysb.export.kappa)
KasaInterfaceError
KasimInterfaceError
keys() (pysb.core.ComponentSet method)
L
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)
Model (class in pysb.core)
model (pysb.export.Exporter attribute)
ModelAssertion (class in pysb.testing.modeltests)
ModelAssertionFailure
ModelExistsWarning
ModelNotDefinedError
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)
MultiState (class in pysb.core)
N
Name (class in pysb.pattern)
O
Observable (class in pysb.core)
odes (pysb.core.Model attribute)
OdeView (class in pysb.core)
P
pad() (in module pysb.export)
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)
Pattern (class in pysb.pattern)
pore_bind() (in module pysb.macros)
pore_transport() (in module pysb.macros)
pysb.core (module)
pysb.export (module)
pysb.export.kappa (module)
pysb.export.pysb_flat (module)
pysb.kappa (module)
pysb.macros (module)
pysb.pattern (module)
pysb.testing.modeltests (module)
PysbFlatExporter (class in pysb.export.pysb_flat)
R
ReactionAssertion (class in pysb.testing.modeltests)
ReactionNetworkAssertion (class in pysb.testing.modeltests)
ReactionPattern (class in pysb.core)
ReactionPatternMatcher (class in pysb.pattern)
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)
run_simulation() (in module pysb.kappa)
run_static_analysis() (in module pysb.kappa)
S
SelfExporter (class in pysb.core)
set_kappa_path() (in module pysb.kappa)
SimulationResult (class in pysb.kappa)
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)
stoichiometry_matrix (pysb.core.Model attribute)
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)
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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