Index

_

__abs__() (strengths.UnitValue method) __add__() (strengths.UnitValue method) __eq__() (strengths.UnitValue method) __ge__() (strengths.UnitValue method) __gt__() (strengths.UnitValue method) __le__() (strengths.UnitValue method) __lt__() (strengths.UnitValue method) __mod__() (strengths.UnitValue method) __mul__() (strengths.UnitValue method) __neg__() (strengths.UnitValue method)

__neq__() (strengths.UnitValue method) __pos__() (strengths.UnitValue method) __pow__() (strengths.UnitValue method) __radd__() (strengths.UnitValue method) __rmod__() (strengths.UnitValue method) __rmul__() (strengths.UnitValue method) __rpow__() (strengths.UnitValue method) __rsub__() (strengths.UnitValue method) __rtruediv__() (strengths.UnitValue method) __sub__() (strengths.UnitValue method) __truediv__() (strengths.UnitValue method)

A

apply_reaction() (strengths.RDSystem method) are_neighbors() (strengths.RDGraphSpace method) (strengths.RDGridSpace method)

avogadro_number() (in module strengths.constants)

C

cell_env (strengths.RDGridSpace property) cell_vol (strengths.RDGridSpace property) cgmap (strengths.RDTrajectory property) check() (strengths.RDGraphSpace method) chemostats (strengths.RDSystem property) chstt (strengths.Species property) compute_diffusion_rates() (in module strengths.kinetics) compute_dspeciesdt() (in module strengths.kinetics) compute_dstatedt() (in module strengths.kinetics) compute_reaction_rates() (in module strengths.kinetics) convert() (strengths.UnitArray method) (strengths.UnitValue method)

convert_unitvalue() (in module strengths) convert_value() (in module strengths) copy() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) (strengths.RDNetwork method) (strengths.RDScript method) (strengths.RDSystem method) (strengths.Reaction method) (strengths.Species method) (strengths.UnitArray method) (strengths.Units method) (strengths.UnitValue method)

D

d (strengths.RDGridSpace property) D (strengths.Species property) data (strengths.RDTrajectory property) density (strengths.Species property)

density_units_dimensions() (in module strengths) description (strengths.rdengine.RDEngineBase property) dim (strengths.Units property) dsto() (strengths.Reaction method)

E

edges (strengths.RDGraphSpace property) engine_description (strengths.RDTrajectory property) engine_option (strengths.RDTrajectory property)

environments (strengths.RDNetwork property) equilibrium_constant() (strengths.Reaction method) euler_engine() (in module strengths.engine_collection)

F

finalize() (strengths.rdengine.RDEngineBase method)

G

generate_species_chemostats() (in module strengths) generate_species_state() (in module strengths) generate_system_chemostats() (in module strengths) generate_system_state() (in module strengths) get_at() (strengths.UnitArray method) get_boundary_conditions() (strengths.RDGridSpace method) get_cell_coordinates() (strengths.RDGridSpace method) get_cell_env() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) get_cell_env_array() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) get_cell_index() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) (strengths.RDSystem method) get_cell_vol() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) get_cell_vol_array() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) get_chemostat() (strengths.RDSystem method)

get_edge() (strengths.RDGraphSpace method) get_environment_index() (strengths.RDNetwork method) get_error() (strengths.RDSystem method) get_neighbors() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) get_output() (strengths.rdengine.RDEngineBase method) get_product_stoichiometry() (strengths.Reaction method) get_progress() (strengths.rdengine.RDEngineBase method) get_reaction() (strengths.RDNetwork method) get_reaction_index() (strengths.RDNetwork method) get_sample_index() (strengths.RDTrajectory method) get_species() (strengths.RDNetwork method) get_species_index() (strengths.RDNetwork method) get_state() (strengths.RDSystem method) (strengths.RDTrajectory method) get_state_index() (strengths.RDSystem method) get_substrate_stoichiometry() (strengths.Reaction method) get_trajectory() (strengths.RDTrajectory method) get_trajectory_point() (strengths.RDTrajectory method) gillespie_engine() (in module strengths.engine_collection)

H

h (strengths.RDGridSpace property)

I

init_state_processing (strengths.RDScript property) invert() (strengths.UnitArray method) (strengths.Units method) (strengths.UnitValue method)

is_complete() (strengths.rdengine.RDEngineBase method) is_valid() (strengths.RDSystem method) is_within_bounds() (strengths.RDGridSpace method) iterate() (strengths.rdengine.RDEngineBase method) iterate_n() (strengths.rdengine.RDEngineBase method)

K

K (strengths.Reaction property) kf (strengths.Reaction property)

kf_units_dimensions() (strengths.Reaction method) kr (strengths.Reaction property) kr_units_dimensions() (strengths.Reaction method)

L

label (strengths.Reaction property) (strengths.Species property) load_rdnetwork() (in module strengths)

load_rdscript() (in module strengths) load_rdspace() (in module strengths) load_rdsystem() (in module strengths) load_rdtrajectory() (in module strengths)

M

make_dxdtf() (strengths.RDSystem method)

multiply() (strengths.Units method)

N

ncells() (strengths.RDTrajectory method) nenvironments() (strengths.RDNetwork method) network (strengths.RDSystem property) nodes (strengths.RDGraphSpace property)

nreactions() (strengths.RDNetwork method) nsamples() (strengths.RDTrajectory method) nspecies() (strengths.RDNetwork method) (strengths.RDTrajectory method)

O

option (strengths.rdengine.RDEngineBase property)

order() (strengths.Reaction method)

P

parse_units() (in module strengths) parse_unitvalue() (in module strengths) plot_chemostats_2D() (in module strengths.plot) plot_environments_2D() (in module strengths.plot)

plot_sample_state_2D() (in module strengths.plot) plot_state_2D() (in module strengths.plot) plot_trajectory() (in module strengths.plot) products (strengths.Reaction property) psto() (strengths.Reaction method)

Q

quantity_units_dimensions() (in module strengths)

R

raiseto() (strengths.Units method) RDEngineBase (class in strengths.rdengine) RDGraphSpace (class in strengths) RDGridSpace (class in strengths) RDNetwork (class in strengths) rdnetwork_from_dict() (in module strengths) rdnetwork_to_dict() (in module strengths) RDScript (class in strengths) rdscript_from_dict() (in module strengths) rdscript_to_dict() (in module strengths) rdspace_from_dict() (in module strengths)

rdspace_to_dict() (in module strengths) RDSystem (class in strengths) rdsystem_from_dict() (in module strengths) rdsystem_to_dict() (in module strengths) RDTrajectory (class in strengths) Reaction (class in strengths) reactions (strengths.RDNetwork property) reset_chemostats() (strengths.RDSystem method) reset_state() (strengths.RDSystem method) rng_seed (strengths.RDScript property) rorder() (strengths.Reaction method) run() (strengths.rdengine.RDEngineBase method)

S

sample() (strengths.rdengine.RDEngineBase method) sampling_interval (strengths.RDScript property) sampling_policy (strengths.RDScript property) save_rdnetwork() (in module strengths) save_rdscript() (in module strengths) save_rdspace() (in module strengths) save_rdsystem() (in module strengths) save_rdtrajectory() (in module strengths) script (strengths.RDTrajectory property) set_at() (strengths.UnitArray method) set_boundary_conditions() (strengths.RDGridSpace method) set_chemostat() (strengths.RDSystem method) set_default_chemostats() (strengths.RDSystem method) set_default_state() (strengths.RDSystem method) set_k() (strengths.Reaction method) set_state() (strengths.RDSystem method) set_value() (strengths.UnitArray method)

setup() (strengths.rdengine.RDEngineBase method) simulate() (in module strengths) simulate_script() (in module strengths) size() (strengths.RDGraphSpace method) (strengths.RDGridSpace method) space (strengths.RDSystem property) space_units_dimensions() (in module strengths) Species (class in strengths) species (strengths.RDNetwork property) species_labels() (strengths.RDNetwork method) split() (strengths.Reaction method) ssto() (strengths.Reaction method) state (strengths.RDSystem property) state_size() (strengths.RDSystem method) substrates (strengths.Reaction property) sys (strengths.Units property) system (strengths.RDScript property) (strengths.RDTrajectory property)

T

t (strengths.RDTrajectory property) t_max (strengths.RDScript property) t_sample (strengths.RDScript property)

tauleap_engine() (in module strengths.engine_collection) time_step (strengths.RDScript property) time_units_dimensions() (in module strengths) to_string() (strengths.Reaction method)

U

UnitArray (class in strengths) unitarray_from_dict() (in module strengths) unitarray_to_dict() (in module strengths) Units (class in strengths) units (strengths.UnitArray property) (strengths.UnitValue property) units_system (strengths.RDGraphSpace property) (strengths.RDGridSpace property) (strengths.RDNetwork property) (strengths.RDScript property) (strengths.RDSystem property) (strengths.Reaction property) (strengths.Species property)

UnitsDimensions (class in strengths) unitsdimensions_from_dict() (in module strengths) UnitsSystem (class in strengths) unitssystem_from_dict() (in module strengths) UnitValue (class in strengths)

V

value (strengths.UnitArray property) (strengths.UnitValue property)

volume_units_dimensions() (in module strengths)

W

w (strengths.RDGridSpace property)