Index

A

add() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_assignment() (gillespy2.core.Event method) (gillespy2.core.events.Event method) add_assignment_rule() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_event() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_function_definition() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_parameter() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_product() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) add_rate_rule() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_reactant() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method)

add_reaction() (gillespy2.core.Model method) (gillespy2.core.model.Model method) add_species() (gillespy2.core.Model method) (gillespy2.core.model.Model method) addProduct() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) addReactant() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) Annotate() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) append() (gillespy2.core.UserList method) arange() (gillespy2.core.TimeSpan class method) (gillespy2.core.timespan.TimeSpan class method) AssignmentRule (class in gillespy2.core) (class in gillespy2.core.assignmentrule) AssignmentRuleError, [1] astimezone() (gillespy2.core.datetime method) average_ensemble() (gillespy2.core.Results method) (gillespy2.core.results.Results method)

B

BasicSimDecoder (class in gillespy2.solvers.cpp.c_decoder) build_cache() (gillespy2.solvers.cpp.build.build_engine.BuildEngine method) build_engine (gillespy2.solvers.cpp.ode_c_solver.ODECSolver attribute) (gillespy2.solvers.cpp.ODECSolver attribute) (gillespy2.solvers.cpp.ssa_c_solver.SSACSolver attribute) (gillespy2.solvers.cpp.SSACSolver attribute) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver attribute) (gillespy2.solvers.cpp.tau_leaping_c_solver.TauLeapingCSolver attribute) (gillespy2.solvers.cpp.TauHybridCSolver attribute) (gillespy2.solvers.cpp.TauLeapingCSolver attribute)

build_from_solver_results() (gillespy2.core.Results class method) (gillespy2.core.results.Results class method) build_simulation() (gillespy2.solvers.cpp.build.build_engine.BuildEngine method) (gillespy2.solvers.cpp.build.make.Make method) BuildEngine (class in gillespy2.solvers.cpp.build.build_engine) BuildError, [1]

C

ChainMap (class in gillespy2.core) change_param_values() (in module gillespy2.solvers.utilities.solverutils) check_blacklist() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) check_cpp_support() (in module gillespy2.solvers.utilities.cpp_support_test) clean() (gillespy2.solvers.cpp.build.build_engine.BuildEngine method) cleanup_tempfiles() (in module gillespy2.core) (in module gillespy2.core.cleanup) clear() (gillespy2.core.ChainMap method) (gillespy2.core.OrderedDict method) (gillespy2.core.UserList method) CLESolver (class in gillespy2.solvers) (class in gillespy2.solvers.numpy) (class in gillespy2.solvers.numpy.CLE_solver) combine() (gillespy2.core.datetime method) common_rgb_values() (in module gillespy2.core) (in module gillespy2.core.results)

compile_prep() (gillespy2.core.Model method) (gillespy2.core.model.Model method) ComplexJsonCoder (class in gillespy2.core.jsonify) convert_str() (gillespy2.solvers.cpp.build.expression.ExpressionConverter class method) copy() (gillespy2.core.ChainMap method) (gillespy2.core.OrderedDict method) (gillespy2.core.UserDict method) (gillespy2.core.UserList method) count() (gillespy2.core.UserList method) CppConverter (class in gillespy2.solvers.cpp.build.expression) CppConverter.CppExpressionTransformer (class in gillespy2.solvers.cpp.build.expression) create_default() (gillespy2.solvers.cpp.c_decoder.SimDecoder class method) create_mass_action() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) CRepeatTimer (class in gillespy2.core.liveGraphing) CSolver (class in gillespy2.solvers.cpp.c_solver) ctime() (gillespy2.core.datetime method)

D

date() (gillespy2.core.datetime method) datetime (class in gillespy2.core) decode() (gillespy2.core.jsonify.ComplexJsonCoder method) default() (gillespy2.core.jsonify.ComplexJsonCoder method) delete_all_assignment_rules() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_all_events() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_all_function_definitions() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_all_parameters() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_all_rate_rules() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_all_reactions() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_all_species() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_assignment_rule() (gillespy2.core.Model method) (gillespy2.core.model.Model method)

delete_event() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_function_definition() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_parameter() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_rate_rule() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_reaction() (gillespy2.core.Model method) (gillespy2.core.model.Model method) delete_species() (gillespy2.core.Model method) (gillespy2.core.model.Model method) dependency_grapher() (in module gillespy2.solvers.utilities.solverutils) DirectoryError, [1] display() (gillespy2.core.liveGraphing.LiveDisplayer method) display_types() (in module gillespy2.core.liveGraphing) DONE (gillespy2.solvers.cpp.c_solver.SimulationReturnCode attribute) dst() (gillespy2.core.datetime method)

E

Event (class in gillespy2.core) (class in gillespy2.core.events) EventAssignment (class in gillespy2.core) (class in gillespy2.core.events) EventError, [1] EventTrigger (class in gillespy2.core) (class in gillespy2.core.events) ExecutionError, [1] export() (in module gillespy2.stochss.StochSSexport)

export_SBML() (in module gillespy2.core) (in module gillespy2.core.model) export_StochSS() (in module gillespy2.core) (in module gillespy2.core.model) Expression (class in gillespy2.solvers.cpp.build.expression) Expression.ValidationVisitor (class in gillespy2.solvers.cpp.build.expression) ExpressionConverter (class in gillespy2.solvers.cpp.build.expression) ExpressionResults (class in gillespy2.solvers.cpp.build.expression) extend() (gillespy2.core.UserList method)

F

FAILED (gillespy2.solvers.cpp.c_solver.SimulationReturnCode attribute) fold (gillespy2.core.datetime attribute) from_dict() (gillespy2.core.Jsonify class method) (gillespy2.core.jsonify.Jsonify class method) from_file() (gillespy2.core.model.StochMLDocument class method) (gillespy2.core.StochMLDocument class method) from_json() (gillespy2.core.Jsonify class method) (gillespy2.core.jsonify.Int64Coder static method) (gillespy2.core.jsonify.Jsonify class method) (gillespy2.core.jsonify.NdArrayCoder static method) (gillespy2.core.jsonify.SetCoder static method) (gillespy2.core.jsonify.TypeCoder static method) (gillespy2.core.Reaction class method) (gillespy2.core.reaction.Reaction class method)

from_model() (gillespy2.core.model.StochMLDocument class method) (gillespy2.core.StochMLDocument class method) from_string() (gillespy2.core.model.StochMLDocument class method) (gillespy2.core.StochMLDocument class method) fromisoformat() (gillespy2.core.datetime method) fromkeys() (gillespy2.core.ChainMap class method) (gillespy2.core.OrderedDict method) (gillespy2.core.UserDict class method) fromtimestamp() (gillespy2.core.datetime method) function_map (gillespy2.solvers.cpp.build.template_gen.SanitizedModel attribute) FunctionDefinition (class in gillespy2.core) (class in gillespy2.core.functiondefinition) FunctionDefinitionError, [1]

G

get() (gillespy2.core.ChainMap method) get_all_assignment_rules() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_all_events() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_all_function_definitions() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_all_parameters() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_all_rate_rules() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_all_reactions() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_all_species() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_arg_string() (gillespy2.core.FunctionDefinition method) (gillespy2.core.functiondefinition.FunctionDefinition method) get_assignment_rule() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_best_solver() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_best_solver_algo() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_element() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_event() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_executable_path() (gillespy2.solvers.cpp.build.build_engine.BuildEngine method) get_function_definition() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_json_hash() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) get_missing_dependencies() (gillespy2.solvers.cpp.build.build_engine.BuildEngine class method) get_model_defines() (in module gillespy2.solvers.cpp.build.template_gen) get_model_features() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_options() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method) get_output() (gillespy2.solvers.cpp.c_decoder.BasicSimDecoder method) (gillespy2.solvers.cpp.c_decoder.IterativeSimDecoder method) (gillespy2.solvers.cpp.c_decoder.SimDecoder method) get_parameter() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_rate_rule() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_reaction() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_solver_settings() (gillespy2.core.GillesPySolver method) (gillespy2.core.gillespySolver.GillesPySolver method) (gillespy2.solvers.CLESolver class method) (gillespy2.solvers.cpp.ode_c_solver.ODECSolver class method) (gillespy2.solvers.cpp.ODECSolver class method) (gillespy2.solvers.cpp.ssa_c_solver.SSACSolver class method) (gillespy2.solvers.cpp.SSACSolver class method) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver class method) (gillespy2.solvers.cpp.tau_leaping_c_solver.TauLeapingCSolver class method) (gillespy2.solvers.cpp.TauHybridCSolver class method) (gillespy2.solvers.cpp.TauLeapingCSolver class method) (gillespy2.solvers.numpy.CLE_solver.CLESolver class method) (gillespy2.solvers.numpy.CLESolver class method) (gillespy2.solvers.numpy.NumPySSASolver class method) (gillespy2.solvers.numpy.ode_solver.ODESolver class method) (gillespy2.solvers.numpy.ODESolver class method) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver class method) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver class method) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver class method) (gillespy2.solvers.numpy.TauHybridSolver class method) (gillespy2.solvers.numpy.TauLeapingSolver class method) (gillespy2.solvers.NumPySSASolver class method) (gillespy2.solvers.ODECSolver class method) (gillespy2.solvers.ODESolver class method) (gillespy2.solvers.SSACSolver class method) (gillespy2.solvers.TauHybridCSolver class method) (gillespy2.solvers.TauHybridSolver class method) (gillespy2.solvers.TauLeapingCSolver class method) (gillespy2.solvers.TauLeapingSolver class method) get_species() (gillespy2.core.Model method) (gillespy2.core.model.Model method) get_str() (gillespy2.solvers.cpp.build.expression.CppConverter method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) get_supported_features() (gillespy2.core.GillesPySolver class method) (gillespy2.core.gillespySolver.GillesPySolver class method) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver class method) (gillespy2.solvers.cpp.TauHybridCSolver class method) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver class method) (gillespy2.solvers.numpy.TauHybridSolver class method) (gillespy2.solvers.TauHybridCSolver class method) (gillespy2.solvers.TauHybridSolver class method) get_supported_integrator_options() (gillespy2.core.GillesPySolver class method) (gillespy2.core.gillespySolver.GillesPySolver class method) (gillespy2.solvers.cpp.ode_c_solver.ODECSolver static method) (gillespy2.solvers.cpp.ODECSolver static method) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver class method) (gillespy2.solvers.cpp.TauHybridCSolver class method) (gillespy2.solvers.ODECSolver static method) (gillespy2.solvers.TauHybridCSolver class method)

get_template() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method) get_translation_table() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) getexpr_cpp() (gillespy2.solvers.cpp.build.expression.Expression method) getexpr_python() (gillespy2.solvers.cpp.build.expression.Expression method) gillespy2 module gillespy2.core module gillespy2.core.assignmentrule module gillespy2.core.cleanup module gillespy2.core.events module gillespy2.core.functiondefinition module gillespy2.core.gillespyError module gillespy2.core.gillespySolver module gillespy2.core.jsonify module gillespy2.core.liveGraphing module gillespy2.core.model module gillespy2.core.parameter module gillespy2.core.raterule module gillespy2.core.reaction module gillespy2.core.results module gillespy2.core.sortableobject module gillespy2.core.species module gillespy2.core.timespan module gillespy2.sbml module gillespy2.solvers module gillespy2.solvers.cpp module gillespy2.solvers.cpp.build module gillespy2.solvers.cpp.build.build_engine module gillespy2.solvers.cpp.build.expression module gillespy2.solvers.cpp.build.make module gillespy2.solvers.cpp.build.template_gen module gillespy2.solvers.cpp.c_decoder module gillespy2.solvers.cpp.c_solver module gillespy2.solvers.cpp.ode_c_solver module gillespy2.solvers.cpp.ssa_c_solver module gillespy2.solvers.cpp.tau_hybrid_c_solver module gillespy2.solvers.cpp.tau_leaping_c_solver module gillespy2.solvers.numpy module gillespy2.solvers.numpy.CLE_solver module gillespy2.solvers.numpy.ode_solver module gillespy2.solvers.numpy.ssa_solver module gillespy2.solvers.numpy.tau_hybrid_solver module gillespy2.solvers.numpy.tau_leaping_solver module gillespy2.solvers.utilities module gillespy2.solvers.utilities.cpp_support_test module gillespy2.solvers.utilities.solverutils module gillespy2.solvers.utilities.Tau module gillespy2.stochss module gillespy2.stochss.StochSSexport module GillesPySolver (class in gillespy2.core) (class in gillespy2.core.gillespySolver)

H

hour (gillespy2.core.datetime attribute)

I

import_SBML() (in module gillespy2.core) (in module gillespy2.core.model) increment_trajectory() (gillespy2.core.liveGraphing.LiveDisplayer method) index() (gillespy2.core.UserList method) initialize() (in module gillespy2.solvers.utilities.Tau) insert() (gillespy2.core.UserList method) Int64Coder (class in gillespy2.core.jsonify) INTEGRATOR_FAILED (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.cpp.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.TauHybridCSolver.ErrorStatus attribute)

INVALID_AFTER_SSA (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.cpp.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.TauHybridCSolver.ErrorStatus attribute) InvalidModelError, [1] InvalidStochMLError, [1] isoformat() (gillespy2.core.datetime method) items() (gillespy2.core.OrderedDict method) IterativeSimDecoder (class in gillespy2.solvers.cpp.c_decoder)

J

Jsonify (class in gillespy2.core) (class in gillespy2.core.jsonify)

K

keys() (gillespy2.core.OrderedDict method)

L

linspace() (gillespy2.core.TimeSpan class method) (gillespy2.core.timespan.TimeSpan class method) LiveDisplayer (class in gillespy2.core.liveGraphing)

LOOP_OVER_INTEGRATE (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.cpp.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.TauHybridCSolver.ErrorStatus attribute)

M

Make (class in gillespy2.solvers.cpp.build.make) make_translation_table() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) (gillespy2.core.Model method) (gillespy2.core.model.Model method) map_operator() (gillespy2.solvers.cpp.build.expression.Expression class method) max (gillespy2.core.datetime attribute) microsecond (gillespy2.core.datetime attribute) min (gillespy2.core.datetime attribute) minute (gillespy2.core.datetime attribute) Model (class in gillespy2.core) (class in gillespy2.core.model) ModelError, [1] module gillespy2 gillespy2.core gillespy2.core.assignmentrule gillespy2.core.cleanup gillespy2.core.events gillespy2.core.functiondefinition gillespy2.core.gillespyError gillespy2.core.gillespySolver gillespy2.core.jsonify gillespy2.core.liveGraphing gillespy2.core.model gillespy2.core.parameter gillespy2.core.raterule gillespy2.core.reaction gillespy2.core.results gillespy2.core.sortableobject gillespy2.core.species gillespy2.core.timespan gillespy2.sbml gillespy2.solvers gillespy2.solvers.cpp gillespy2.solvers.cpp.build gillespy2.solvers.cpp.build.build_engine gillespy2.solvers.cpp.build.expression gillespy2.solvers.cpp.build.make gillespy2.solvers.cpp.build.template_gen gillespy2.solvers.cpp.c_decoder gillespy2.solvers.cpp.c_solver gillespy2.solvers.cpp.ode_c_solver gillespy2.solvers.cpp.ssa_c_solver gillespy2.solvers.cpp.tau_hybrid_c_solver gillespy2.solvers.cpp.tau_leaping_c_solver gillespy2.solvers.numpy gillespy2.solvers.numpy.CLE_solver gillespy2.solvers.numpy.ode_solver gillespy2.solvers.numpy.ssa_solver gillespy2.solvers.numpy.tau_hybrid_solver gillespy2.solvers.numpy.tau_leaping_solver gillespy2.solvers.utilities gillespy2.solvers.utilities.cpp_support_test gillespy2.solvers.utilities.solverutils gillespy2.solvers.utilities.Tau gillespy2.stochss gillespy2.stochss.StochSSexport

move_to_end() (gillespy2.core.OrderedDict method)

N

name (gillespy2.core.GillesPySolver attribute) (gillespy2.core.gillespySolver.GillesPySolver attribute) (gillespy2.solvers.CLESolver attribute) (gillespy2.solvers.cpp.ode_c_solver.ODECSolver attribute) (gillespy2.solvers.cpp.ODECSolver attribute) (gillespy2.solvers.cpp.ssa_c_solver.SSACSolver attribute) (gillespy2.solvers.cpp.SSACSolver attribute) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver attribute) (gillespy2.solvers.cpp.tau_leaping_c_solver.TauLeapingCSolver attribute) (gillespy2.solvers.cpp.TauHybridCSolver attribute) (gillespy2.solvers.cpp.TauLeapingCSolver attribute) (gillespy2.solvers.numpy.CLE_solver.CLESolver attribute) (gillespy2.solvers.numpy.CLESolver attribute) (gillespy2.solvers.numpy.NumPySSASolver attribute) (gillespy2.solvers.numpy.ode_solver.ODESolver attribute) (gillespy2.solvers.numpy.ODESolver attribute) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver attribute) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver attribute) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver attribute) (gillespy2.solvers.numpy.TauHybridSolver attribute) (gillespy2.solvers.numpy.TauLeapingSolver attribute) (gillespy2.solvers.NumPySSASolver attribute) (gillespy2.solvers.ODECSolver attribute) (gillespy2.solvers.ODESolver attribute) (gillespy2.solvers.SSACSolver attribute) (gillespy2.solvers.TauHybridCSolver attribute) (gillespy2.solvers.TauHybridSolver attribute) (gillespy2.solvers.TauLeapingCSolver attribute) (gillespy2.solvers.TauLeapingSolver attribute)

NdArrayCoder (class in gillespy2.core.jsonify) NEGATIVE_STATE_AT_BEGINING_OF_STEP (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.cpp.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.TauHybridCSolver.ErrorStatus attribute) NEGATIVE_STATE_NO_SSA_REACTION (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.cpp.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.TauHybridCSolver.ErrorStatus attribute) new_child() (gillespy2.core.ChainMap method) now() (gillespy2.core.datetime method) numpy_initialization() (in module gillespy2.solvers.utilities.solverutils) numpy_resume() (in module gillespy2.solvers.utilities.solverutils) numpy_trajectory_base_initialization() (in module gillespy2.solvers.utilities.solverutils) NumPySSASolver (class in gillespy2.solvers) (class in gillespy2.solvers.numpy) (class in gillespy2.solvers.numpy.ssa_solver)

O

obj_to_anon() (gillespy2.core.jsonify.TranslationTable method) (gillespy2.core.TranslationTable method) obj_to_named() (gillespy2.core.jsonify.TranslationTable method) (gillespy2.core.TranslationTable method) ODECSolver (class in gillespy2.solvers) (class in gillespy2.solvers.cpp) (class in gillespy2.solvers.cpp.ode_c_solver)

ODESolver (class in gillespy2.solvers) (class in gillespy2.solvers.numpy) (class in gillespy2.solvers.numpy.ode_solver) operator_map (gillespy2.solvers.cpp.build.expression.Expression attribute) OrderedDict (class in gillespy2.core)

P

Parameter (class in gillespy2.core) (class in gillespy2.core.parameter) ParameterError, [1] parents (gillespy2.core.ChainMap property) parse_comparison() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) parse_logical() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) parse_operator() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) pause (gillespy2.core.liveGraphing.CRepeatTimer attribute) (gillespy2.core.liveGraphing.RepeatTimer attribute) pause_event (gillespy2.solvers.CLESolver attribute) (gillespy2.solvers.numpy.CLE_solver.CLESolver attribute) (gillespy2.solvers.numpy.CLESolver attribute) (gillespy2.solvers.numpy.NumPySSASolver attribute) (gillespy2.solvers.numpy.ode_solver.ODESolver attribute) (gillespy2.solvers.numpy.ODESolver attribute) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver attribute) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver attribute) (gillespy2.solvers.numpy.TauLeapingSolver attribute) (gillespy2.solvers.NumPySSASolver attribute) (gillespy2.solvers.ODESolver attribute) (gillespy2.solvers.TauLeapingSolver attribute) PAUSED (gillespy2.solvers.cpp.c_solver.SimulationReturnCode attribute) plot() (gillespy2.core.Results method) (gillespy2.core.results.Results method)

plot_mean_stdev() (gillespy2.core.Results method) (gillespy2.core.results.Results method) plot_std_dev_range() (gillespy2.core.Results method) (gillespy2.core.results.Results method) plotplotly() (gillespy2.core.Results method) (gillespy2.core.results.Results method) plotplotly_mean_stdev() (gillespy2.core.Results method) (gillespy2.core.results.Results method) plotplotly_std_dev_range() (gillespy2.core.Results method) (gillespy2.core.results.Results method) pop() (gillespy2.core.ChainMap method) (gillespy2.core.OrderedDict method) (gillespy2.core.UserList method) popitem() (gillespy2.core.ChainMap method) (gillespy2.core.OrderedDict method) prebuild() (gillespy2.solvers.cpp.build.make.Make method) prepare() (gillespy2.solvers.cpp.build.build_engine.BuildEngine method) print_text_header() (gillespy2.core.liveGraphing.LiveDisplayer method) problem_with_name() (gillespy2.core.Model method) (gillespy2.core.model.Model method) public_vars() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) PythonConverter (class in gillespy2.solvers.cpp.build.expression)

R

RateRule (class in gillespy2.core) (class in gillespy2.core.raterule) RateRuleError, [1] rc (gillespy2.solvers.CLESolver attribute) (gillespy2.solvers.cpp.c_solver.CSolver attribute) (gillespy2.solvers.numpy.CLE_solver.CLESolver attribute) (gillespy2.solvers.numpy.CLESolver attribute) (gillespy2.solvers.numpy.NumPySSASolver attribute) (gillespy2.solvers.numpy.ode_solver.ODESolver attribute) (gillespy2.solvers.numpy.ODESolver attribute) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver attribute) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver attribute) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver attribute) (gillespy2.solvers.numpy.TauHybridSolver attribute) (gillespy2.solvers.numpy.TauLeapingSolver attribute) (gillespy2.solvers.NumPySSASolver attribute) (gillespy2.solvers.ODESolver attribute) (gillespy2.solvers.TauHybridSolver attribute) (gillespy2.solvers.TauLeapingSolver attribute) Reaction (class in gillespy2.core) (class in gillespy2.core.reaction) ReactionError, [1] read() (gillespy2.solvers.cpp.c_decoder.BasicSimDecoder method) (gillespy2.solvers.cpp.c_decoder.IterativeSimDecoder method) (gillespy2.solvers.cpp.c_decoder.SimDecoder method) recursive_translate() (gillespy2.core.jsonify.TranslationTable method) (gillespy2.core.TranslationTable method) remove() (gillespy2.core.UserList method) RepeatTimer (class in gillespy2.core.liveGraphing) replace() (gillespy2.core.datetime method) reserved_names (gillespy2.core.Model attribute) (gillespy2.core.model.Model attribute) (gillespy2.solvers.cpp.build.template_gen.SanitizedModel attribute) resolution (gillespy2.core.datetime attribute) result (gillespy2.solvers.CLESolver attribute) (gillespy2.solvers.numpy.CLE_solver.CLESolver attribute) (gillespy2.solvers.numpy.CLESolver attribute) (gillespy2.solvers.numpy.NumPySSASolver attribute) (gillespy2.solvers.numpy.ode_solver.ODESolver attribute) (gillespy2.solvers.numpy.ODESolver attribute) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver attribute) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver attribute) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver attribute) (gillespy2.solvers.numpy.TauHybridSolver attribute) (gillespy2.solvers.numpy.TauLeapingSolver attribute) (gillespy2.solvers.NumPySSASolver attribute) (gillespy2.solvers.ODESolver attribute) (gillespy2.solvers.TauHybridSolver attribute) (gillespy2.solvers.TauLeapingSolver attribute)

Results (class in gillespy2.core) (class in gillespy2.core.results) ResultsError, [1] reverse() (gillespy2.core.UserList method) run() (gillespy2.core.GillesPySolver method) (gillespy2.core.gillespySolver.GillesPySolver method) (gillespy2.core.liveGraphing.CRepeatTimer method) (gillespy2.core.liveGraphing.RepeatTimer method) (gillespy2.core.Model method) (gillespy2.core.model.Model method) (gillespy2.solvers.CLESolver method) (gillespy2.solvers.cpp.ode_c_solver.ODECSolver method) (gillespy2.solvers.cpp.ODECSolver method) (gillespy2.solvers.cpp.ssa_c_solver.SSACSolver method) (gillespy2.solvers.cpp.SSACSolver method) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver method) (gillespy2.solvers.cpp.tau_leaping_c_solver.TauLeapingCSolver method) (gillespy2.solvers.cpp.TauHybridCSolver method) (gillespy2.solvers.cpp.TauLeapingCSolver method) (gillespy2.solvers.numpy.CLE_solver.CLESolver method) (gillespy2.solvers.numpy.CLESolver method) (gillespy2.solvers.numpy.NumPySSASolver method) (gillespy2.solvers.numpy.ode_solver.ODESolver method) (gillespy2.solvers.numpy.ODESolver method) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver method) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver method) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver method) (gillespy2.solvers.numpy.TauHybridSolver method) (gillespy2.solvers.numpy.TauLeapingSolver method) (gillespy2.solvers.NumPySSASolver method) (gillespy2.solvers.ODECSolver method) (gillespy2.solvers.ODESolver method) (gillespy2.solvers.SSACSolver method) (gillespy2.solvers.TauHybridCSolver method) (gillespy2.solvers.TauHybridSolver method) (gillespy2.solvers.TauLeapingCSolver method) (gillespy2.solvers.TauLeapingSolver method)

S

sanitized_expression() (gillespy2.core.events.EventTrigger method) (gillespy2.core.EventTrigger method) (gillespy2.core.Parameter method) (gillespy2.core.parameter.Parameter method) sanitized_formula() (gillespy2.core.AssignmentRule method) (gillespy2.core.assignmentrule.AssignmentRule method) (gillespy2.core.RateRule method) (gillespy2.core.raterule.RateRule method) sanitized_function() (gillespy2.core.FunctionDefinition method) (gillespy2.core.functiondefinition.FunctionDefinition method) sanitized_parameter_names() (gillespy2.core.Model method) (gillespy2.core.model.Model method) sanitized_propensity_function() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) sanitized_species_names() (gillespy2.core.Model method) (gillespy2.core.model.Model method) SanitizedModel (class in gillespy2.solvers.cpp.build.template_gen) SBMLError, [1] second (gillespy2.core.datetime attribute) select() (in module gillespy2.solvers.utilities.Tau) serialize() (gillespy2.core.Model method) (gillespy2.core.model.Model method) set_annotation() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) set_initial_value() (gillespy2.core.Species method) (gillespy2.core.species.Species method) set_parameter() (gillespy2.core.Model method) (gillespy2.core.model.Model method) set_propensities() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) set_rate() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) set_units() (gillespy2.core.Model method) (gillespy2.core.model.Model method) SetCoder (class in gillespy2.core.jsonify) setdefault() (gillespy2.core.OrderedDict method) setType() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method)

SimDecoder (class in gillespy2.solvers.cpp.c_decoder) SimulationError, [1] SimulationReturnCode (class in gillespy2.solvers.cpp.c_solver) SimulationTimeoutError, [1] SolverError, [1] sort() (gillespy2.core.UserList method) SortableObject (class in gillespy2.core) (class in gillespy2.core.sortableobject) special_characters (gillespy2.core.Model attribute) (gillespy2.core.model.Model attribute) Species (class in gillespy2.core) (class in gillespy2.core.species) species_parse() (in module gillespy2.solvers.utilities.solverutils) SpeciesError, [1] SSACSolver (class in gillespy2.solvers) (class in gillespy2.solvers.cpp) (class in gillespy2.solvers.cpp.ssa_c_solver) stddev_ensemble() (gillespy2.core.Results method) (gillespy2.core.results.Results method) StochMLDocument (class in gillespy2.core) (class in gillespy2.core.model) StochMLImportError, [1] stop_event (gillespy2.solvers.CLESolver attribute) (gillespy2.solvers.numpy.CLE_solver.CLESolver attribute) (gillespy2.solvers.numpy.CLESolver attribute) (gillespy2.solvers.numpy.NumPySSASolver attribute) (gillespy2.solvers.numpy.ode_solver.ODESolver attribute) (gillespy2.solvers.numpy.ODESolver attribute) (gillespy2.solvers.numpy.ssa_solver.NumPySSASolver attribute) (gillespy2.solvers.numpy.tau_hybrid_solver.TauHybridSolver attribute) (gillespy2.solvers.numpy.tau_leaping_solver.TauLeapingSolver attribute) (gillespy2.solvers.numpy.TauHybridSolver attribute) (gillespy2.solvers.numpy.TauLeapingSolver attribute) (gillespy2.solvers.NumPySSASolver attribute) (gillespy2.solvers.ODESolver attribute) (gillespy2.solvers.TauHybridSolver attribute) (gillespy2.solvers.TauLeapingSolver attribute) strptime() (gillespy2.core.datetime method)

T

target (gillespy2.solvers.cpp.ode_c_solver.ODECSolver attribute) (gillespy2.solvers.cpp.ODECSolver attribute) (gillespy2.solvers.cpp.ssa_c_solver.SSACSolver attribute) (gillespy2.solvers.cpp.SSACSolver attribute) (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver attribute) (gillespy2.solvers.cpp.tau_leaping_c_solver.TauLeapingCSolver attribute) (gillespy2.solvers.cpp.TauHybridCSolver attribute) (gillespy2.solvers.cpp.TauLeapingCSolver attribute) (gillespy2.solvers.ODECSolver attribute) (gillespy2.solvers.SSACSolver attribute) (gillespy2.solvers.TauHybridCSolver attribute) (gillespy2.solvers.TauLeapingCSolver attribute) TauHybridCSolver (class in gillespy2.solvers) (class in gillespy2.solvers.cpp) (class in gillespy2.solvers.cpp.tau_hybrid_c_solver) TauHybridCSolver.ErrorStatus (class in gillespy2.solvers) (class in gillespy2.solvers.cpp) (class in gillespy2.solvers.cpp.tau_hybrid_c_solver) TauHybridSolver (class in gillespy2.solvers) (class in gillespy2.solvers.numpy) (class in gillespy2.solvers.numpy.tau_hybrid_solver) TauLeapingCSolver (class in gillespy2.solvers) (class in gillespy2.solvers.cpp) (class in gillespy2.solvers.cpp.tau_leaping_c_solver) TauLeapingSolver (class in gillespy2.solvers) (class in gillespy2.solvers.numpy) (class in gillespy2.solvers.numpy.tau_leaping_solver) template_def_propensities() (in module gillespy2.solvers.cpp.build.template_gen) template_def_rate_rules() (in module gillespy2.solvers.cpp.build.template_gen) template_def_reactions() (in module gillespy2.solvers.cpp.build.template_gen) template_def_species() (in module gillespy2.solvers.cpp.build.template_gen) template_def_variables() (in module gillespy2.solvers.cpp.build.template_gen) template_definitions_name (gillespy2.solvers.cpp.build.build_engine.BuildEngine attribute) template_options_name (gillespy2.solvers.cpp.build.build_engine.BuildEngine attribute) time() (gillespy2.core.datetime method) TimeSpan (class in gillespy2.core) (class in gillespy2.core.timespan)

timespan() (gillespy2.core.Model method) (gillespy2.core.model.Model method) TimespanError, [1] timestamp() (gillespy2.core.datetime method) timetuple() (gillespy2.core.datetime method) timetz() (gillespy2.core.datetime method) to_anon() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) to_array() (gillespy2.core.Results method) (gillespy2.core.results.Results method) to_csv() (gillespy2.core.Results method) (gillespy2.core.results.Results method) to_dict() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Int64Coder static method) (gillespy2.core.jsonify.Jsonify method) (gillespy2.core.jsonify.NdArrayCoder static method) (gillespy2.core.jsonify.SetCoder static method) (gillespy2.core.jsonify.TypeCoder static method) (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) to_json() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) to_model() (gillespy2.core.model.StochMLDocument method) (gillespy2.core.StochMLDocument method) to_named() (gillespy2.core.Jsonify method) (gillespy2.core.jsonify.Jsonify method) to_string() (gillespy2.core.model.StochMLDocument method) (gillespy2.core.StochMLDocument method) Trajectory (class in gillespy2.core) (class in gillespy2.core.results) trajectory_header() (gillespy2.core.liveGraphing.LiveDisplayer method) TranslationTable (class in gillespy2.core) (class in gillespy2.core.jsonify) TypeCoder (class in gillespy2.core.jsonify) tzinfo (gillespy2.core.datetime attribute) tzname() (gillespy2.core.datetime method)

U

UNKNOWN (gillespy2.solvers.cpp.tau_hybrid_c_solver.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.cpp.TauHybridCSolver.ErrorStatus attribute) (gillespy2.solvers.TauHybridCSolver.ErrorStatus attribute) update() (gillespy2.core.OrderedDict method) update_model_options() (in module gillespy2.solvers.cpp.build.template_gen) update_namespace() (gillespy2.core.Model method) (gillespy2.core.model.Model method) update_species_init_values() (in module gillespy2.solvers.utilities.solverutils)

use_propensity() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method) use_rate_rule() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method) use_reaction() (gillespy2.solvers.cpp.build.template_gen.SanitizedModel method) UserDict (class in gillespy2.core) UserList (class in gillespy2.core) utcfromtimestamp() (gillespy2.core.datetime method) utcnow() (gillespy2.core.datetime method) utcoffset() (gillespy2.core.datetime method) utctimetuple() (gillespy2.core.datetime method)

V

valid_graph_params() (in module gillespy2.core.liveGraphing) validate() (gillespy2.core.Parameter method) (gillespy2.core.parameter.Parameter method) (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) (gillespy2.core.Species method) (gillespy2.core.species.Species method) (gillespy2.core.TimeSpan method) (gillespy2.core.timespan.TimeSpan method) (gillespy2.solvers.cpp.build.expression.Expression method) validate_integrator_options() (gillespy2.core.GillesPySolver class method) (gillespy2.core.gillespySolver.GillesPySolver class method) validate_model() (gillespy2.core.GillesPySolver class method) (gillespy2.core.gillespySolver.GillesPySolver class method) validate_reactants_and_products() (gillespy2.core.Model method) (gillespy2.core.model.Model method) validate_sbml_features() (gillespy2.core.GillesPySolver class method) (gillespy2.core.gillespySolver.GillesPySolver class method) validate_tspan() (gillespy2.core.GillesPySolver method) (gillespy2.core.gillespySolver.GillesPySolver method) ValidationError, [1] values() (gillespy2.core.OrderedDict method) verify() (gillespy2.core.Reaction method) (gillespy2.core.reaction.Reaction method) visit_Add() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_And() (gillespy2.solvers.cpp.build.expression.CppConverter method) (gillespy2.solvers.cpp.build.expression.PythonConverter method) visit_Assign() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) visit_BinOp() (gillespy2.solvers.cpp.build.expression.CppConverter.CppExpressionTransformer method) (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method)

visit_BoolOp() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Bytes() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Call() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Compare() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Constant() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Div() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Ellipsis() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Eq() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Gt() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_GtE() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Lt() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_LtE() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Mult() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Name() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_NameConstant() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_NotEq() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Num() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Or() (gillespy2.solvers.cpp.build.expression.CppConverter method) (gillespy2.solvers.cpp.build.expression.PythonConverter method) visit_Pow() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Str() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_Sub() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_UnaryOp() (gillespy2.solvers.cpp.build.expression.Expression.ValidationVisitor method) (gillespy2.solvers.cpp.build.expression.ExpressionConverter method) visit_USub() (gillespy2.solvers.cpp.build.expression.ExpressionConverter method)

W

with_blacklist() (gillespy2.solvers.cpp.build.expression.Expression method) with_callback() (gillespy2.solvers.cpp.c_decoder.IterativeSimDecoder method)

with_namespace() (gillespy2.solvers.cpp.build.expression.Expression method) write_definitions() (in module gillespy2.solvers.cpp.build.template_gen) write_template() (in module gillespy2.solvers.cpp.build.template_gen)