Index

A

add_ensemble() (gillespy.gillespy.StochKitOutputCollection method) add_parameter() (gillespy.gillespy.Model method) add_reaction() (gillespy.gillespy.Model method) add_species() (gillespy.gillespy.Model method)

add_trajectory() (gillespy.gillespy.StochKitEnsemble method) addProduct() (gillespy.gillespy.Reaction method) addReactant() (gillespy.gillespy.Reaction method) Annotate() (gillespy.gillespy.Reaction method)

C

create_mass_action() (gillespy.gillespy.Reaction method)

D

delete_all_parameters() (gillespy.gillespy.Model method) delete_all_reactions() (gillespy.gillespy.Model method) delete_all_species() (gillespy.gillespy.Model method) delete_parameter() (gillespy.gillespy.Model method)

delete_reaction() (gillespy.gillespy.Model method) delete_species() (gillespy.gillespy.Model method) dump() (gillespy.gillespy.StochKitEnsemble method)

E

evaluate() (gillespy.gillespy.Parameter method)

F

from_file() (gillespy.gillespy.StochMLDocument class method) from_model() (gillespy.gillespy.StochMLDocument class method)

from_string() (gillespy.gillespy.StochMLDocument class method)

G

get_all_parameters() (gillespy.gillespy.Model method) get_all_reactions() (gillespy.gillespy.Model method) get_all_species() (gillespy.gillespy.Model method) get_parameter() (gillespy.gillespy.Model method) get_reaction() (gillespy.gillespy.Model method)

get_species() (gillespy.gillespy.Model method) gillespy (module) gillespy.gillespy (module) GillesPySolver (class in gillespy.gillespy)

I

InvalidStochMLError

M

Model (class in gillespy.gillespy)

ModelError

P

Parameter (class in gillespy.gillespy) parameter_to_element() (gillespy.gillespy.StochMLDocument method)

ParameterError

R

Reaction (class in gillespy.gillespy) reaction_to_element() (gillespy.gillespy.StochMLDocument method) ReactionError

resolve_parameters() (gillespy.gillespy.Model method) run() (gillespy.gillespy.GillesPySolver class method) (gillespy.gillespy.StochKitODESolver class method) (gillespy.gillespy.StochKitSolver class method)

S

serialize() (gillespy.gillespy.Model method) set_expression() (gillespy.gillespy.Parameter method) set_parameter() (gillespy.gillespy.Model method) set_units() (gillespy.gillespy.Model method) setType() (gillespy.gillespy.Reaction method) SimuliationError Species (class in gillespy.gillespy) species_to_element() (gillespy.gillespy.StochMLDocument method)

SpeciesError StochKitEnsemble (class in gillespy.gillespy) StochKitODESolver (class in gillespy.gillespy) StochKitOutputCollection (class in gillespy.gillespy) StochKitSolver (class in gillespy.gillespy) StochKitTrajectory (class in gillespy.gillespy) StochMLDocument (class in gillespy.gillespy) StochMLImportError

T

to_model() (gillespy.gillespy.StochMLDocument method)

to_string() (gillespy.gillespy.StochMLDocument method)

U

update_namespace() (gillespy.gillespy.Model method)