Index

A

add_config() (ppsim.simulation.Simulation method) add_snapshot() (ppsim.simulation.Simulation method)

array_from_dict() (ppsim.simulation.Simulation method) ax (ppsim.snapshot.Plotter attribute)

C

categories (ppsim.snapshot.Plotter attribute) column_names (ppsim.simulation.Simulation attribute) concentration_to_count() (in module ppsim.crn) config (ppsim.snapshot.Snapshot attribute)

config_array (ppsim.simulation.Simulation property) config_dict (ppsim.simulation.Simulation property) configs (ppsim.simulation.Simulation attribute) continuous_time (ppsim.simulation.Simulation attribute) convert_unimolecular_to_bimolecular_and_flip_reactant_order() (in module ppsim.crn)

E

enabled_reactions (ppsim.simulation.Simulation property)

Expression (class in ppsim.crn)

F

fig (ppsim.snapshot.Plotter attribute)

G

get_species() (ppsim.crn.Expression method) (ppsim.crn.Reaction method)

gillespy2_format() (in module ppsim.crn) gpac_format() (in module ppsim.crn)

H

history (ppsim.simulation.Simulation property)

HistoryPlotter (class in ppsim.snapshot)

I

initialize() (ppsim.snapshot.Plotter method) (ppsim.snapshot.Snapshot method) (ppsim.snapshot.StatePlotter method) (ppsim.snapshot.TimeUpdate method)

initialize_simulator() (ppsim.simulation.Simulation method) is_bimolecular() (ppsim.crn.Reaction method) is_conservative() (ppsim.crn.Reaction method) is_unimolecular() (ppsim.crn.Reaction method)

K

k() (ppsim.crn.Reaction method)

M

mass_action (ppsim.crn.RateConstantUnits attribute) module ppsim ppsim.crn, [1] ppsim.simulation, [1] ppsim.snapshot, [1]

N

name (ppsim.crn.Specie attribute) next_snapshot_time (ppsim.snapshot.Snapshot attribute)

null_probability (ppsim.simulation.Simulation property) num_products() (ppsim.crn.Reaction method) num_reactants() (ppsim.crn.Reaction method)

P

pbar (ppsim.snapshot.TimeUpdate attribute) Plotter (class in ppsim.snapshot) ppsim module ppsim.crn module, [1] ppsim.simulation module, [1]

ppsim.snapshot module, [1] product_if_unique() (ppsim.crn.Reaction method) product_names_if_exactly_two() (ppsim.crn.Reaction method) products (ppsim.crn.Reaction attribute) products_if_exactly_two() (ppsim.crn.Reaction method)

R

r() (ppsim.crn.Reaction method) rate_constant (ppsim.crn.Reaction attribute) rate_constant_reverse (ppsim.crn.Reaction attribute) rate_constant_reverse_stochastic (ppsim.crn.Reaction property) rate_constant_reverse_units (ppsim.crn.Reaction attribute) rate_constant_stochastic (ppsim.crn.Reaction property) rate_constant_units (ppsim.crn.Reaction attribute) RateConstantUnits (class in ppsim.crn) reactant_if_unimolecular() (ppsim.crn.Reaction method) reactant_names_if_bimolecular() (ppsim.crn.Reaction method) reactants (ppsim.crn.Reaction attribute)

reactants_if_bimolecular() (ppsim.crn.Reaction method) Reaction (class in ppsim.crn) reactions (ppsim.simulation.Simulation property) reactions_to_dict() (in module ppsim.crn) replace_reversible_rxns() (in module ppsim.crn) reset() (ppsim.simulation.Simulation method) reversible (ppsim.crn.Reaction attribute) rng (ppsim.simulation.Simulation attribute) Rule (in module ppsim.simulation) rule() (ppsim.simulation.Simulation method) run() (ppsim.simulation.Simulation method)

S

sample_future_configuration() (ppsim.simulation.Simulation method) sample_silence_time() (ppsim.simulation.Simulation method) seed (ppsim.simulation.Simulation attribute) set_config() (ppsim.simulation.Simulation method) set_snapshot_index() (ppsim.simulation.Simulation method) set_snapshot_time() (ppsim.simulation.Simulation method) silent() (ppsim.simulation.Simulation method) Simulation (class in ppsim.simulation) simulation (ppsim.snapshot.Snapshot attribute) simulator (ppsim.simulation.Simulation attribute) simulator_method (ppsim.simulation.Simulation attribute) Snapshot (class in ppsim.snapshot) snapshot_slider() (ppsim.simulation.Simulation method) snapshots (ppsim.simulation.Simulation attribute)

Specie (class in ppsim.crn) species (ppsim.crn.Expression attribute) species() (in module ppsim.crn) species_in_rxns() (in module ppsim.crn) start_time (ppsim.snapshot.TimeUpdate attribute) state_dict (ppsim.simulation.Simulation attribute) state_enumeration() (in module ppsim.simulation) state_list (ppsim.simulation.Simulation attribute) state_map (ppsim.snapshot.Plotter attribute) StatePlotter (class in ppsim.snapshot) steps_per_time_unit (ppsim.simulation.Simulation attribute) stochastic (ppsim.crn.RateConstantUnits attribute) stochkit_format() (in module ppsim.crn) symmetric() (ppsim.crn.Reaction method) symmetric_products() (ppsim.crn.Reaction method)

T

time (ppsim.simulation.Simulation attribute) (ppsim.snapshot.Snapshot attribute) time_to_steps() (ppsim.simulation.Simulation method) time_trials() (in module ppsim.simulation)

time_units (ppsim.simulation.Simulation attribute) times (ppsim.simulation.Simulation attribute) times_in_units() (ppsim.simulation.Simulation method) TimeUpdate (class in ppsim.snapshot)

U

update() (ppsim.snapshot.HistoryPlotter method) (ppsim.snapshot.Snapshot method) (ppsim.snapshot.StatePlotter method) (ppsim.snapshot.TimeUpdate method)

update_time (ppsim.snapshot.Snapshot attribute)

W

write_stochkit_file() (in module ppsim.crn)

Y

yscale (ppsim.snapshot.Plotter attribute)