Index

A

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

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

B

batss module batss.crn module

batss.simulation module batss.snapshot module

C

catalyst_specie() (in module batss.crn) categories (batss.snapshot.Plotter attribute) column_names (batss.simulation.Simulation attribute) concentration_to_count() (in module batss.crn) config (batss.snapshot.Snapshot attribute) config_array (batss.simulation.Simulation property)

config_dict (batss.simulation.Simulation property) configs (batss.simulation.Simulation attribute) continuous_time (batss.simulation.Simulation attribute) convert_to_uniform() (in module batss.crn) convert_unimolecular_to_bimolecular_and_flip_reactant_order() (in module batss.crn) CRN (class in batss.crn)

D

discrete_steps_no_nulls (batss.simulation.Simulation attribute) discrete_steps_no_nulls_last_run (batss.simulation.Simulation attribute)

discrete_steps_total (batss.simulation.Simulation attribute) discrete_steps_total_last_run (batss.simulation.Simulation attribute)

E

enabled_reactions (batss.simulation.Simulation property) exportable_reactions() (batss.crn.CRN method)

Expression (class in batss.crn) extra_species() (in module batss.crn)

F

fig (batss.snapshot.Plotter attribute)

G

generativity() (batss.crn.CRN method) (batss.crn.Reaction method) get_species() (batss.crn.Expression method) (batss.crn.Reaction method)

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

H

history (batss.simulation.Simulation property)

HistoryPlotter (class in batss.snapshot)

I

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

initialize_simulator() (batss.simulation.Simulation method) is_bimolecular() (batss.crn.Reaction method) is_conservative() (batss.crn.Reaction method) is_special_specie (batss.crn.Specie attribute) is_unimolecular() (batss.crn.Reaction method)

K

k() (batss.crn.Reaction method)

M

mass_action (batss.crn.RateConstantUnits attribute) module batss batss.crn batss.simulation batss.snapshot

N

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

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

O

order() (batss.crn.CRN method)

P

pbar (batss.snapshot.TimeUpdate attribute) Plotter (class in batss.snapshot) product_if_unique() (batss.crn.Reaction method)

product_names_if_exactly_two() (batss.crn.Reaction method) products (batss.crn.Reaction attribute) products_if_exactly_two() (batss.crn.Reaction method)

R

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

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

S

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

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

T

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

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

U

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

update_time (batss.snapshot.Snapshot attribute)

W

waste_specie() (in module batss.crn)

write_stochkit_file() (in module batss.crn)

Y

yscale (batss.snapshot.Plotter attribute)