ppsim
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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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Q
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R
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S
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T
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U
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W
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Y
_
_matrix (ppsim.snapshot.Plotter attribute)
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)
B
batch_threshold (ppsim.simulator.SimulatorMultiBatch attribute)
bitgen (ppsim.simulator.Simulator attribute)
(ppsim.simulator.Urn attribute)
C
categories (ppsim.snapshot.Plotter attribute)
coll_table (ppsim.simulator.SimulatorMultiBatch attribute)
coll_table_r_values (ppsim.simulator.SimulatorMultiBatch attribute)
coll_table_u_values (ppsim.simulator.SimulatorMultiBatch attribute)
column_names (ppsim.simulation.Simulation attribute)
concentration_to_count() (in module ppsim.crn)
config (ppsim.simulator.Simulator attribute)
(ppsim.simulator.Urn attribute)
(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)
D
do_gillespie (ppsim.simulator.SimulatorMultiBatch attribute)
E
enabled_reactions (ppsim.simulation.Simulation property)
(ppsim.simulator.SimulatorMultiBatch attribute)
Expression (class in ppsim.crn)
F
fig (ppsim.snapshot.Plotter attribute)
G
gen (ppsim.simulator.Simulator attribute)
get_enabled_reactions() (ppsim.simulator.SimulatorMultiBatch method)
get_species() (ppsim.crn.Expression method)
(ppsim.crn.Reaction method)
get_total_propensity() (ppsim.simulator.SimulatorMultiBatch method)
gillespie_step() (ppsim.simulator.SimulatorMultiBatch method)
gillespie_threshold (ppsim.simulator.SimulatorMultiBatch attribute)
gillespy2_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_random (ppsim.simulator.Simulator attribute)
is_unimolecular() (ppsim.crn.Reaction method)
K
k() (ppsim.crn.Reaction method)
L
length (ppsim.simulator.Urn attribute)
logn (ppsim.simulator.SimulatorMultiBatch attribute)
M
m (ppsim.simulator.SimulatorMultiBatch attribute)
make_population() (ppsim.simulator.SimulatorSequentialArray method)
mass_action (ppsim.crn.RateConstantUnits attribute)
module
ppsim.crn
ppsim.simulation
ppsim.simulator
ppsim.snapshot
multibatch_step() (ppsim.simulator.SimulatorMultiBatch method)
N
n (ppsim.simulator.Simulator attribute)
null_probability (ppsim.simulation.Simulation property)
num_enabled_reactions (ppsim.simulator.SimulatorMultiBatch attribute)
num_products() (ppsim.crn.Reaction method)
num_r_values (ppsim.simulator.SimulatorMultiBatch attribute)
num_reactants() (ppsim.crn.Reaction method)
num_u_values (ppsim.simulator.SimulatorMultiBatch attribute)
O
order (ppsim.simulator.Urn attribute)
P
Plotter (class in ppsim.snapshot)
population (ppsim.simulator.SimulatorSequentialArray attribute)
ppsim.crn
module
ppsim.simulation
module
ppsim.simulator
module
ppsim.snapshot
module
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)
propensities (ppsim.simulator.SimulatorMultiBatch attribute)
Q
q (ppsim.simulator.Simulator attribute)
R
r() (ppsim.crn.Reaction method)
r_constant (ppsim.simulator.SimulatorMultiBatch attribute)
random_depth (ppsim.simulator.Simulator attribute)
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)
reaction_probabilities (ppsim.simulator.SimulatorMultiBatch attribute)
reactions (ppsim.simulation.Simulation property)
(ppsim.simulator.SimulatorMultiBatch attribute)
reactions_to_dict() (in module ppsim.crn)
replace_reversible_rxns() (in module ppsim.crn)
reset() (ppsim.simulation.Simulation method)
(ppsim.simulator.Simulator method)
(ppsim.simulator.SimulatorMultiBatch method)
(ppsim.simulator.SimulatorSequentialArray method)
reversible (ppsim.crn.Reaction attribute)
rng (ppsim.simulation.Simulation attribute)
row (ppsim.simulator.SimulatorMultiBatch attribute)
row_sums (ppsim.simulator.SimulatorMultiBatch attribute)
Rule (in module ppsim.simulation)
rule() (ppsim.simulation.Simulation method)
run() (ppsim.simulation.Simulation method)
(ppsim.simulator.Simulator method)
(ppsim.simulator.SimulatorMultiBatch method)
(ppsim.simulator.SimulatorSequentialArray method)
run_until_silent() (ppsim.simulator.SimulatorMultiBatch 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_n_parameters() (ppsim.simulator.SimulatorMultiBatch method)
set_snapshot_index() (ppsim.simulation.Simulation method)
set_snapshot_time() (ppsim.simulation.Simulation method)
silent (ppsim.simulator.SimulatorMultiBatch attribute)
Simulation (class in ppsim.simulation)
simulation (ppsim.snapshot.Snapshot attribute)
Simulator (class in ppsim.simulator)
simulator (ppsim.simulation.Simulation attribute)
SimulatorMultiBatch (class in ppsim.simulator)
SimulatorSequentialArray (class in ppsim.simulator)
size (ppsim.simulator.Urn attribute)
Snapshot (class in ppsim.snapshot)
snapshot_slider() (ppsim.simulation.Simulation method)
snapshots (ppsim.simulation.Simulation attribute)
sort_by (ppsim.snapshot.Plotter attribute)
Specie (class in ppsim.crn)
species (ppsim.crn.Expression attribute)
species() (in module ppsim.crn)
species_in_rxns() (in module ppsim.crn)
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
t (ppsim.simulator.Simulator attribute)
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)
updated_counts (ppsim.simulator.SimulatorMultiBatch attribute)
Urn (class in ppsim.simulator)
urn (ppsim.simulator.SimulatorMultiBatch attribute)
W
write_stochkit_file() (in module ppsim.crn)
Y
yscale (ppsim.snapshot.Plotter attribute)
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