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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)
all (pysb.simulator.SimulationResult attribute)
all_component_sets() (pysb.core.Model method)
all_components() (pysb.core.Model method)
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)
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)
cleanup() (pysb.core.SelfExporter static method)
Compartment (class in pysb.core)
CompartmentAlreadySpecifiedError
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
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)
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)
Exporter (class in pysb.export)
Expression (class in pysb.core)
ExpressionError
expressions (pysb.simulator.SimulationResult attribute)
expressions_constant() (pysb.core.Model method)
expressions_dynamic() (pysb.core.Model method)
extract_site_conditions() (in module pysb.core)
F
flux_map (pysb.kappa.SimulationResult attribute)
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_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_bngl() (pysb.bng.BngConsole method)
M
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)
ModelExistsWarning
Monomer (class in pysb.core)
MonomerPattern (class in pysb.core)
N
net_filename (pysb.bng.BngBaseInterface attribute)
NoInitialConditionsError
NoRulesError
nsims (pysb.simulator.SimulationResult attribute)
O
Observable (class in pysb.core)
observables (pysb.simulator.SimulationResult attribute)
odesolve() (in module pysb.integrate)
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)
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.importers.bngl (module)
pysb.importers.sbml (module)
pysb.integrate (module)
pysb.kappa (module)
pysb.macros (module)
pysb.simulator (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
ReactionPattern (class in pysb.core)
read_netfile() (pysb.bng.BngBaseInterface method)
read_simulation_results() (pysb.bng.BngBaseInterface 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)
RuleExpression (class in pysb.core)
run() (in module pysb.tools.render_reactions)
(in module pysb.tools.render_species)
(pysb.integrate.Solver 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
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_kappa_path() (in module pysb.kappa)
setup_module() (in module pysb.integrate)
SimulationResult (class in pysb.kappa)
(class in pysb.simulator)
Solver (class in pysb.integrate)
species (pysb.simulator.SimulationResult attribute)
StaticAnalysisResult (class in pysb.kappa)
StochKitSimulator (class in pysb.simulator)
SymbolExistsWarning
synthesize() (in module pysb.macros)
synthesize_degrade_table() (in module pysb.macros)
T
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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