E-Cell4
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
X
|
Y
|
Z
A
AABB (class in ecell4_base.core)
absolute_tolerance() (ecell4_base.ode.ODESimulator method)
accumulation() (ecell4_base.core.TimeoutObserver method)
add_molecules() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.gillespie.GillespieWorld method)
(ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.ode.ODEWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
add_offlattice() (ecell4_base.spatiocyte.SpatiocyteWorld method)
add_potential() (ecell4_base.egfrd.BDSimulator method)
add_product() (ecell4_base.core.ReactionRule method)
add_reactant() (ecell4_base.core.ReactionRule method)
add_reaction_rule() (ecell4_base.core.Model method)
add_reaction_rules() (ecell4_base.core.Model method)
add_site() (ecell4_base.core.UnitSpecies method)
add_species_attribute() (ecell4_base.core.Model method)
add_species_attributes() (ecell4_base.core.Model method)
add_structure() (ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
add_unit() (ecell4_base.core.Species method)
adjoining_pairs() (ecell4_base.spatiocyte.OffLattice method)
AffineTransformation (class in ecell4_base.core)
another() (ecell4_base.core.Complement method)
(ecell4_base.core.Union method)
apply_boundary() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
apply_species_attributes() (ecell4_base.core.Model method)
area() (ecell4_base.core.Triangle method)
as_string() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.ReactionRuleDescriptorPyfunc method)
Ascii (ecell4_base.core.STLFormat attribute)
Attriubte (class in ecell4_base.core)
axis() (ecell4_base.core.Cylinder method)
(ecell4_base.core.CylindricalSurface method)
B
Barycentric (class in ecell4_base.core)
BDFactory (class in ecell4_base.bd)
(class in ecell4_base.egfrd)
BDSimulator (class in ecell4_base.bd)
(class in ecell4_base.egfrd)
BDWorld (class in ecell4_base.bd)
Binary (ecell4_base.core.STLFormat attribute)
bind_to() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.gillespie.GillespieWorld method)
(ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.ode.ODEWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
binomial() (ecell4_base.core.RandomNumberGenerator method)
C
calculate_hcp_lengths() (ecell4_base.spatiocyte.SpatiocyteWorld static method)
calculate_shape() (ecell4_base.spatiocyte.SpatiocyteWorld static method)
calculate_volume() (ecell4_base.spatiocyte.SpatiocyteWorld static method)
calculate_voxel_volume() (ecell4_base.spatiocyte.SpatiocyteWorld static method)
cbrt() (in module ecell4_base.core)
center() (ecell4_base.core.Cylinder method)
(ecell4_base.core.CylindricalSurface method)
(ecell4_base.core.Sphere method)
(ecell4_base.core.SphericalSurface method)
check_model() (in module ecell4.extra.unit)
check_reaction() (ecell4_base.core.Simulator method)
check_structure() (ecell4_base.meso.MesoscopicWorld method)
citation() (in module ecell4.datasource)
clear() (ecell4_base.core.UnitSpecies method)
col() (ecell4_base.core.Integer3 property)
Complement (class in ecell4_base.core)
coord2global() (ecell4_base.meso.MesoscopicWorld method)
coordinate() (ecell4_base.meso.ReactionInfo method)
count() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.Species method)
count_species_matches() (in module ecell4_base.core)
create_binding_reaction_rule() (in module ecell4_base.core)
create_degradation_reaction_rule() (in module ecell4_base.core)
create_spatiocyte_world_cell_list_impl() (in module ecell4_base.spatiocyte)
create_spatiocyte_world_square_offlattice_impl() (in module ecell4_base.spatiocyte)
create_spatiocyte_world_vector_impl() (in module ecell4_base.spatiocyte)
create_synthesis_reaction_rule() (in module ecell4_base.core)
create_unbinding_reaction_rule() (in module ecell4_base.core)
create_unimolecular_reaction_rule() (in module ecell4_base.core)
create_x_plane() (in module ecell4_base.core)
create_y_plane() (in module ecell4_base.core)
create_z_plane() (in module ecell4_base.core)
cross_product() (in module ecell4_base.core)
CSVObserver (class in ecell4_base.core)
Cylinder (class in ecell4_base.core)
CylindricalSurface (class in ecell4_base.core)
D
D() (ecell4_base.core.Particle method)
(ecell4_base.core.Species method)
data() (ecell4_base.core.FixedIntervalNumberObserver method)
(ecell4_base.core.FixedIntervalTrackingObserver method)
(ecell4_base.core.FixedIntervalTrajectoryObserver method)
(ecell4_base.core.NumberObserver method)
(ecell4_base.core.TimingNumberObserver method)
(ecell4_base.core.TimingTrajectoryObserver method)
derivatives() (ecell4_base.ode.ODESimulator method)
description() (in module ecell4.datasource)
deserialize() (ecell4_base.core.UnitSpecies method)
DESTROY (ecell4_base.core.ReactionRule attribute)
(ecell4_base.core.ReactionRule.ReactionRulePolicy attribute)
dimension() (ecell4_base.core.Shape method)
(ecell4_base.core.Species method)
DimensionalityMismatchError
display_pdb() (in module ecell4.plotting)
distance() (ecell4_base.bd.BDWorld method)
(ecell4_base.core.AABB method)
(ecell4_base.core.Cylinder method)
(ecell4_base.core.CylindricalSurface method)
(ecell4_base.core.Rod method)
(ecell4_base.core.RodSurface method)
(ecell4_base.core.Sphere method)
(ecell4_base.core.SphericalSurface method)
(ecell4_base.egfrd.EGFRDWorld method)
distance_sq() (ecell4_base.bd.BDWorld method)
dot_product() (in module ecell4_base.core)
dt() (ecell4_base.core.Simulator method)
dt_factor() (ecell4_base.egfrd.BDSimulator method)
duration() (ecell4_base.core.TimeoutObserver method)
E
e0() (ecell4_base.core.PlanarSurface method)
e1() (ecell4_base.core.PlanarSurface method)
ecell4
module
ecell4.datasource
module
ecell4.extra.ensemble
module
ecell4.extra.unit
module
ecell4.mca
module
ecell4.plotting
module
ecell4.util
module
ecell4_base
module
ecell4_base.bd
module
ecell4_base.core
module
ecell4_base.egfrd
module
ecell4_base.gillespie
module
ecell4_base.meso
module
ecell4_base.ode
module
ecell4_base.spatiocyte
module
edge_lengths() (ecell4_base.core.MeshSurface method)
(ecell4_base.core.WorldInterface method)
effective() (ecell4_base.core.NetfreeModel method)
EGFRDFactory (class in ecell4_base.egfrd)
EGFRDSimulator (class in ecell4_base.egfrd)
EGFRDWorld (class in ecell4_base.egfrd)
elasticity() (ecell4_base.ode.ODESimulator method)
ensemble() (ecell4.util.Session method)
ensemble_simulations() (in module ecell4.util)
EULER (ecell4_base.ode.ODESolverType attribute)
evaluate() (ecell4_base.ode.ODEWorld method)
expand() (ecell4_base.core.Model method)
F
FaceID (class in ecell4_base.core)
Factory (in module ecell4_base.bd)
(in module ecell4_base.egfrd)
(in module ecell4_base.gillespie)
(in module ecell4_base.meso)
(in module ecell4_base.ode)
(in module ecell4_base.spatiocyte)
filename() (ecell4_base.core.CSVObserver method)
(ecell4_base.core.FixedIntervalCSVObserver method)
(ecell4_base.core.FixedIntervalHDF5Observer method)
(ecell4_base.core.MeshSurface method)
first() (ecell4_base.core.AffineTransformation method)
FixedIntervalCSVObserver (class in ecell4_base.core)
FixedIntervalEvent (class in ecell4_base.core)
FixedIntervalHDF5Observer (class in ecell4_base.core)
FixedIntervalNumberObserver (class in ecell4_base.core)
FixedIntervalPythonHooker (class in ecell4_base.core)
FixedIntervalTrackingObserver (class in ecell4_base.core)
FixedIntervalTrajectoryObserver (class in ecell4_base.core)
fluxes() (ecell4_base.ode.ODESimulator method)
format_species() (in module ecell4_base.core)
G
gaussian() (ecell4_base.core.RandomNumberGenerator method)
generate() (ecell4_base.core.ReactionRule method)
generate_full_rank_matrix() (in module ecell4.mca)
genseeds() (in module ecell4.extra.ensemble)
get() (ecell4_base.core.ReactionRuleDescriptorPyfunc method)
get_application_registry() (in module ecell4.extra.unit)
get_attribute() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.Species method)
get_data() (ecell4_base.meso.MesoscopicWorld method)
get_descriptor() (ecell4_base.core.ReactionRule method)
get_dimension_from_model() (in module ecell4_base.core)
get_k() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.ReactionRuleDescriptorMassAction method)
get_model() (in module ecell4.util)
get_occupancy() (ecell4_base.meso.MesoscopicWorld method)
get_particle() (ecell4_base.core.WorldInterface method)
get_site() (ecell4_base.core.UnitSpecies method)
get_species_at() (ecell4_base.spatiocyte.SpatiocyteWorld method)
get_stoichiometry() (in module ecell4_base.core)
get_value() (ecell4_base.core.WorldInterface method)
get_value_exact() (ecell4_base.core.WorldInterface method)
get_values() (ecell4_base.ode.ODEWorld method)
get_volume() (ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
get_voxel() (ecell4_base.spatiocyte.SpatiocyteWorld method)
get_voxel_at() (ecell4_base.spatiocyte.SpatiocyteWorld method)
get_voxel_near_by() (ecell4_base.spatiocyte.SpatiocyteWorld method)
get_voxel_nearby() (ecell4_base.spatiocyte.SpatiocyteWorld method)
getseed() (in module ecell4.extra.ensemble)
getUnitRegistry() (in module ecell4.extra.unit)
GillespieFactory (class in ecell4_base.gillespie)
GillespieSimulator (class in ecell4_base.gillespie)
GillespieWorld (class in ecell4_base.gillespie)
global2coord() (ecell4_base.meso.MesoscopicWorld method)
GSLRandomNumberGenerator (class in ecell4_base.core)
H
half_height() (ecell4_base.core.Cylinder method)
(ecell4_base.core.CylindricalSurface method)
has_attribute() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.Species method)
has_descriptor() (ecell4_base.core.ReactionRule method)
has_particle() (ecell4_base.core.WorldInterface method)
has_particle_at() (ecell4_base.spatiocyte.SpatiocyteWorld method)
has_reaction_rule() (ecell4_base.core.Model method)
has_site() (ecell4_base.core.UnitSpecies method)
has_species() (ecell4_base.core.WorldInterface method)
has_species_attribute() (ecell4_base.core.Model method)
has_structure() (ecell4_base.meso.MesoscopicWorld method)
has_voxel() (ecell4_base.spatiocyte.SpatiocyteWorld method)
I
IMPLICIT (ecell4_base.core.ReactionRule attribute)
(ecell4_base.core.ReactionRule.ReactionRulePolicy attribute)
initialize() (ecell4_base.core.Simulator method)
inside() (ecell4_base.core.CylindricalSurface method)
(ecell4_base.core.SphericalSurface method)
Integer3 (class in ecell4_base.core)
integer3_abs() (in module ecell4_base.core)
integer3_add() (in module ecell4_base.core)
integer3_dot_product() (in module ecell4_base.core)
integer3_length() (in module ecell4_base.core)
integer3_length_sq() (in module ecell4_base.core)
integer3_multiply() (in module ecell4_base.core)
integer3_subtract() (in module ecell4_base.core)
interval() (ecell4_base.core.TimeoutObserver method)
invdiag() (in module ecell4.mca)
is_inside() (ecell4_base.core.Shape method)
J
jacobian() (ecell4_base.ode.ODESimulator method)
K
k() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.ReactionRuleDescriptorMassAction method)
L
last_reactions() (ecell4_base.bd.BDSimulator method)
(ecell4_base.egfrd.BDSimulator method)
(ecell4_base.egfrd.EGFRDSimulator method)
(ecell4_base.gillespie.GillespieSimulator method)
(ecell4_base.meso.MesoscopicSimulator method)
(ecell4_base.spatiocyte.SpatiocyteSimulator method)
layer() (ecell4_base.core.Integer3 property)
length() (ecell4_base.core.Rod method)
(ecell4_base.core.RodSurface method)
(in module ecell4_base.core)
length_sq() (in module ecell4_base.core)
list_attributes() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.Species method)
list_coordinates() (ecell4_base.meso.MesoscopicWorld method)
list_coordinates_exact() (ecell4_base.meso.MesoscopicWorld method)
list_neighbors() (ecell4_base.spatiocyte.SpatiocyteWorld method)
list_non_structure_particles() (ecell4_base.spatiocyte.SpatiocyteWorld method)
list_particles() (ecell4_base.core.WorldInterface method)
list_particles_exact() (ecell4_base.core.WorldInterface method)
list_particles_within_radius() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
list_species() (ecell4_base.core.Model method)
(ecell4_base.core.WorldInterface method)
list_structure_particles() (ecell4_base.spatiocyte.SpatiocyteWorld method)
load() (ecell4_base.core.RandomNumberGenerator method)
(ecell4_base.core.WorldInterface method)
load_version_information() (in module ecell4_base.core)
load_world() (in module ecell4.util)
location() (ecell4_base.core.Species method)
log() (ecell4_base.core.CSVObserver method)
(ecell4_base.core.FixedIntervalCSVObserver method)
logo() (in module ecell4.plotting)
lot() (ecell4_base.core.ParticleID method)
lower() (ecell4_base.core.AABB method)
M
magnitude() (ecell4_base.core.Quantity_Integer property)
(ecell4_base.core.Quantity_Real property)
matrix_sizes() (ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.meso.MesoscopicWorld method)
maximum_step_interval() (ecell4_base.ode.ODESimulator method)
MeshSurface (class in ecell4_base.core)
MesoscopicFactory (class in ecell4_base.meso)
MesoscopicSimulator (class in ecell4_base.meso)
MesoscopicWorld (class in ecell4_base.meso)
Model (class in ecell4_base.core)
model() (ecell4_base.bd.BDSimulator method)
(ecell4_base.egfrd.BDSimulator method)
(ecell4_base.egfrd.EGFRDSimulator method)
(ecell4_base.gillespie.GillespieSimulator method)
(ecell4_base.meso.MesoscopicSimulator method)
(ecell4_base.ode.ODESimulator method)
(ecell4_base.spatiocyte.SpatiocyteSimulator method)
module
ecell4
ecell4.datasource
ecell4.extra.ensemble
ecell4.extra.unit
ecell4.mca
ecell4.plotting
ecell4.util
ecell4_base
ecell4_base.bd
ecell4_base.core
ecell4_base.egfrd
ecell4_base.gillespie
ecell4_base.meso
ecell4_base.ode
ecell4_base.spatiocyte
N
name() (ecell4_base.core.ReactionRule.ReactionRulePolicy property)
(ecell4_base.core.Shape.dimension_kind property)
(ecell4_base.core.STLFormat property)
(ecell4_base.core.UnitSpecies method)
(ecell4_base.ode.ODESolverType property)
NetfreeModel (class in ecell4_base.core)
NetworkModel (class in ecell4_base.core)
new_particle() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.gillespie.GillespieWorld method)
(ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.ode.ODEWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
new_voxel() (ecell4_base.spatiocyte.SpatiocyteWorld method)
new_voxel_structure() (ecell4_base.spatiocyte.SpatiocyteWorld method)
next_time() (ecell4_base.core.Observer method)
(ecell4_base.core.Simulator method)
normal() (ecell4_base.core.PlanarSurface method)
(ecell4_base.core.Triangle method)
num_molecules() (ecell4_base.core.WorldInterface method)
(ecell4_base.meso.MesoscopicWorld method)
num_molecules_exact() (ecell4_base.core.WorldInterface method)
num_particles() (ecell4_base.core.WorldInterface method)
num_particles_exact() (ecell4_base.core.WorldInterface method)
num_reaction_rules() (ecell4_base.core.Model method)
num_steps() (ecell4_base.core.Observer method)
(ecell4_base.core.Simulator method)
num_subvolumes() (ecell4_base.meso.MesoscopicWorld method)
num_tracers() (ecell4_base.core.FixedIntervalTrackingObserver method)
(ecell4_base.core.FixedIntervalTrajectoryObserver method)
(ecell4_base.core.TimingTrajectoryObserver method)
number_observer() (in module ecell4.util)
NumberLogger (class in ecell4_base.core)
NumberObserver (class in ecell4_base.core)
O
Observer (class in ecell4_base.core)
ODEFactory (class in ecell4_base.ode)
ODESimulator (class in ecell4_base.ode)
ODESolverType (class in ecell4_base.ode)
ODEWorld (class in ecell4_base.ode)
OffLattice (class in ecell4_base.spatiocyte)
on_structure() (ecell4_base.meso.MesoscopicWorld method)
ONE (ecell4_base.core.Shape attribute)
(ecell4_base.core.Shape.dimension_kind attribute)
one() (ecell4_base.core.Complement method)
(ecell4_base.core.Union method)
ones() (in module ecell4_base.core)
origin() (ecell4_base.core.PlanarSurface method)
(ecell4_base.core.Rod method)
(ecell4_base.core.RodSurface method)
P
Particle (class in ecell4_base.core)
ParticleID (class in ecell4_base.core)
periodic_transpose() (ecell4_base.bd.BDWorld method)
pid() (ecell4_base.spatiocyte.ReactionInfoItem property)
PlanarSurface (class in ecell4_base.core)
plot_movie() (in module ecell4.plotting)
plot_movie_with_attractive_mpl() (in module ecell4.plotting)
plot_number_observer() (in module ecell4.plotting)
plot_trajectory() (in module ecell4.plotting)
plot_world() (in module ecell4.plotting)
plot_world_with_attractive_mpl() (in module ecell4.plotting)
policy() (ecell4_base.core.ReactionRule method)
Polygon (class in ecell4_base.core)
position() (ecell4_base.core.Particle method)
(ecell4_base.spatiocyte.Voxel method)
position2coordinate() (ecell4_base.meso.MesoscopicWorld method)
position2global() (ecell4_base.meso.MesoscopicWorld method)
positions() (ecell4_base.spatiocyte.OffLattice method)
prefix() (ecell4_base.core.FixedIntervalHDF5Observer method)
product_coefficients() (ecell4_base.core.ReactionRuleDescriptor method)
products() (ecell4_base.bd.ReactionInfo method)
(ecell4_base.core.ReactionRule method)
(ecell4_base.egfrd.ReactionInfo method)
(ecell4_base.gillespie.ReactionInfo method)
(ecell4_base.meso.ReactionInfo method)
(ecell4_base.spatiocyte.ReactionInfo method)
propensity() (ecell4_base.core.ReactionRuleDescriptor method)
Q
Quantity (in module ecell4_base.core)
Quantity_Integer (class in ecell4_base.core)
Quantity_Real (class in ecell4_base.core)
query_reaction_rules() (ecell4_base.core.Model method)
R
radius() (ecell4_base.core.CylindricalSurface method)
(ecell4_base.core.Particle method)
(ecell4_base.core.Rod method)
(ecell4_base.core.RodSurface method)
(ecell4_base.core.Species method)
(ecell4_base.core.Sphere method)
(ecell4_base.core.SphericalSurface method)
RandomNumberGenerator (class in ecell4_base.core)
reactant_coefficients() (ecell4_base.core.ReactionRuleDescriptor method)
reactants() (ecell4_base.bd.ReactionInfo method)
(ecell4_base.core.ReactionRule method)
(ecell4_base.egfrd.ReactionInfo method)
(ecell4_base.gillespie.ReactionInfo method)
(ecell4_base.meso.ReactionInfo method)
(ecell4_base.spatiocyte.ReactionInfo method)
reaction_rules() (ecell4_base.core.Model method)
ReactionInfo (class in ecell4_base.bd)
(class in ecell4_base.egfrd)
(class in ecell4_base.gillespie)
(class in ecell4_base.meso)
(class in ecell4_base.spatiocyte)
ReactionInfoItem (class in ecell4_base.spatiocyte)
ReactionRule (class in ecell4_base.core)
ReactionRule.ReactionRulePolicy (class in ecell4_base.core)
ReactionRuleDescriptor (class in ecell4_base.core)
ReactionRuleDescriptorMassAction (class in ecell4_base.core)
ReactionRuleDescriptorPyfunc (class in ecell4_base.core)
read_polygon() (in module ecell4_base.core)
Real3 (class in ecell4_base.core)
real3_abs() (in module ecell4_base.core)
real3_add() (in module ecell4_base.core)
real3_divide() (in module ecell4_base.core)
real3_dot_product() (in module ecell4_base.core)
real3_length() (in module ecell4_base.core)
real3_length_sq() (in module ecell4_base.core)
real3_multiply() (in module ecell4_base.core)
real3_subtract() (in module ecell4_base.core)
relative_tolerance() (ecell4_base.ode.ODESimulator method)
release_species() (ecell4_base.ode.ODEWorld method)
remove_attribute() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.Species method)
remove_molecules() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.gillespie.GillespieWorld method)
(ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.ode.ODEWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
remove_particle() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
remove_reaction_rule() (ecell4_base.core.Model method)
remove_species_attribute() (ecell4_base.core.Model method)
remove_voxel() (ecell4_base.spatiocyte.SpatiocyteWorld method)
rescale() (ecell4_base.core.AffineTransformation method)
reserve_species() (ecell4_base.ode.ODEWorld method)
reset() (ecell4_base.core.Observer method)
(ecell4_base.core.Polygon method)
reset_descriptor() (ecell4_base.core.ReactionRule method)
rng() (ecell4_base.bd.BDFactory method)
(ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.BDFactory method)
(ecell4_base.egfrd.EGFRDFactory method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.gillespie.GillespieFactory method)
(ecell4_base.gillespie.GillespieWorld method)
(ecell4_base.meso.MesoscopicFactory method)
(ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.ode.ODEFactory method)
(ecell4_base.spatiocyte.SpatiocyteFactory method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
Rod (class in ecell4_base.core)
RodSurface (class in ecell4_base.core)
root() (ecell4_base.core.AffineTransformation method)
(ecell4_base.core.Surface method)
ROSENBROCK4_CONTROLLER (ecell4_base.ode.ODESolverType attribute)
row() (ecell4_base.core.Integer3 property)
run() (ecell4.util.Session method)
(ecell4_base.bd.BDSimulator method)
(ecell4_base.egfrd.BDSimulator method)
(ecell4_base.egfrd.EGFRDSimulator method)
(ecell4_base.gillespie.GillespieSimulator method)
(ecell4_base.meso.MesoscopicSimulator method)
(ecell4_base.ode.ODESimulator method)
(ecell4_base.spatiocyte.SpatiocyteSimulator method)
run_azure() (in module ecell4.extra.ensemble)
run_ensemble() (in module ecell4.extra.ensemble)
run_multiprocessing() (in module ecell4.extra.ensemble)
run_serial() (in module ecell4.extra.ensemble)
run_sge() (in module ecell4.extra.ensemble)
run_simulation() (in module ecell4.util)
run_slurm() (in module ecell4.extra.ensemble)
RUNGE_KUTTA_CASH_KARP54 (ecell4_base.ode.ODESolverType attribute)
S
save() (ecell4_base.core.FixedIntervalNumberObserver method)
(ecell4_base.core.NumberObserver method)
(ecell4_base.core.RandomNumberGenerator method)
(ecell4_base.core.TimingNumberObserver method)
(ecell4_base.core.WorldInterface method)
scale_control_coefficients() (in module ecell4.mca)
scaled_control_coefficients() (in module ecell4.mca)
second() (ecell4_base.core.AffineTransformation method)
seed() (ecell4_base.core.RandomNumberGenerator method)
serial() (ecell4_base.core.ParticleID method)
(ecell4_base.core.Species method)
(ecell4_base.core.UnitSpecies method)
Session (class in ecell4.util)
set_absolute_tolerance() (ecell4_base.ode.ODESimulator method)
set_attribute() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.Species method)
set_descriptor() (ecell4_base.core.ReactionRule method)
set_dt() (ecell4_base.core.Simulator method)
set_effective() (ecell4_base.core.NetfreeModel method)
set_formatter() (ecell4_base.core.CSVObserver method)
(ecell4_base.core.FixedIntervalCSVObserver method)
set_header() (ecell4_base.core.CSVObserver method)
(ecell4_base.core.FixedIntervalCSVObserver method)
set_k() (ecell4_base.core.ReactionRule method)
(ecell4_base.core.ReactionRuleDescriptorMassAction method)
set_maximum_step_interval() (ecell4_base.ode.ODESimulator method)
set_name() (ecell4_base.core.ReactionRuleDescriptorPyfunc method)
(ecell4_base.core.UnitSpecies method)
set_paranoiac() (ecell4_base.egfrd.EGFRDSimulator method)
set_policy() (ecell4_base.core.ReactionRule method)
set_product_coefficient() (ecell4_base.core.ReactionRuleDescriptor method)
set_product_coefficients() (ecell4_base.core.ReactionRuleDescriptor method)
set_reactant_coefficient() (ecell4_base.core.ReactionRuleDescriptor method)
set_reactant_coefficients() (ecell4_base.core.ReactionRuleDescriptor method)
set_relative_tolerance() (ecell4_base.ode.ODESimulator method)
set_t() (ecell4_base.bd.BDSimulator method)
(ecell4_base.core.WorldInterface method)
(ecell4_base.egfrd.BDSimulator method)
(ecell4_base.egfrd.EGFRDSimulator method)
(ecell4_base.gillespie.GillespieSimulator method)
(ecell4_base.meso.MesoscopicSimulator method)
(ecell4_base.ode.ODESimulator method)
(ecell4_base.spatiocyte.SpatiocyteSimulator method)
set_value() (ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.gillespie.GillespieWorld method)
(ecell4_base.meso.MesoscopicWorld method)
(ecell4_base.ode.ODEWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
set_volume() (ecell4_base.ode.ODEWorld method)
Shape (class in ecell4_base.core)
shape() (ecell4_base.spatiocyte.SpatiocyteWorld method)
Shape.dimension_kind (class in ecell4_base.core)
shift() (ecell4_base.core.AffineTransformation method)
(ecell4_base.core.Rod method)
(ecell4_base.core.RodSurface method)
show() (in module ecell4.util)
Simulator (class in ecell4_base.core)
(in module ecell4_base.bd)
(in module ecell4_base.egfrd)
(in module ecell4_base.gillespie)
(in module ecell4_base.meso)
(in module ecell4_base.ode)
(in module ecell4_base.spatiocyte)
simulator() (ecell4_base.bd.BDFactory method)
(ecell4_base.egfrd.BDFactory method)
(ecell4_base.egfrd.EGFRDFactory method)
(ecell4_base.gillespie.GillespieFactory method)
(ecell4_base.meso.MesoscopicFactory method)
(ecell4_base.ode.ODEFactory method)
(ecell4_base.spatiocyte.SpatiocyteFactory method)
sites() (ecell4_base.core.UnitSpecies method)
size() (ecell4_base.spatiocyte.SpatiocyteWorld method)
SpatiocyteFactory (class in ecell4_base.spatiocyte)
SpatiocyteSimulator (class in ecell4_base.spatiocyte)
SpatiocyteWorld (class in ecell4_base.spatiocyte)
Species (class in ecell4_base.core)
species() (ecell4_base.core.Particle method)
(ecell4_base.spatiocyte.ReactionInfoItem property)
species_attributes() (ecell4_base.core.Model method)
species_attributes_proceed() (ecell4_base.core.Model method)
Sphere (class in ecell4_base.core)
SphericalSurface (class in ecell4_base.core)
step() (ecell4_base.core.Simulator method)
STLFormat (class in ecell4_base.core)
stoichiometry() (ecell4_base.ode.ODESimulator method)
STRICT (ecell4_base.core.ReactionRule attribute)
(ecell4_base.core.ReactionRule.ReactionRulePolicy attribute)
subvolume() (ecell4_base.meso.MesoscopicWorld method)
subvolume_edge_lengths() (ecell4_base.meso.MesoscopicWorld method)
Surface (class in ecell4_base.core)
surface() (ecell4_base.core.AABB method)
(ecell4_base.core.AffineTransformation method)
(ecell4_base.core.Complement method)
(ecell4_base.core.Cylinder method)
(ecell4_base.core.Rod method)
(ecell4_base.core.Sphere method)
(ecell4_base.core.Union method)
T
t() (ecell4_base.bd.ReactionInfo method)
(ecell4_base.core.FixedIntervalTrackingObserver method)
(ecell4_base.core.FixedIntervalTrajectoryObserver method)
(ecell4_base.core.Simulator method)
(ecell4_base.core.TimingTrajectoryObserver method)
(ecell4_base.core.WorldInterface method)
(ecell4_base.egfrd.ReactionInfo method)
(ecell4_base.gillespie.ReactionInfo method)
(ecell4_base.meso.ReactionInfo method)
(ecell4_base.spatiocyte.ReactionInfo method)
targets() (ecell4_base.core.FixedIntervalNumberObserver method)
(ecell4_base.core.NumberObserver method)
(ecell4_base.core.TimingNumberObserver method)
third() (ecell4_base.core.AffineTransformation method)
THREE (ecell4_base.core.Shape attribute)
(ecell4_base.core.Shape.dimension_kind attribute)
TimeoutObserver (class in ecell4_base.core)
TimingEvent (class in ecell4_base.core)
TimingNumberObserver (class in ecell4_base.core)
TimingTrajectoryObserver (class in ecell4_base.core)
translate() (ecell4_base.core.AffineTransformation method)
Triangle (class in ecell4_base.core)
triangles() (ecell4_base.core.Polygon method)
TWO (ecell4_base.core.Shape attribute)
(ecell4_base.core.Shape.dimension_kind attribute)
U
UNDEF (ecell4_base.core.Shape attribute)
(ecell4_base.core.Shape.dimension_kind attribute)
uniform() (ecell4_base.core.RandomNumberGenerator method)
uniform_int() (ecell4_base.core.RandomNumberGenerator method)
Union (class in ecell4_base.core)
units() (ecell4_base.core.Quantity_Integer property)
(ecell4_base.core.Quantity_Real property)
(ecell4_base.core.Species method)
UnitSpecies (class in ecell4_base.core)
unitx() (in module ecell4_base.core)
unity() (in module ecell4_base.core)
unitz() (in module ecell4_base.core)
unscaled_control_coefficients() (in module ecell4.mca)
update_particle() (ecell4_base.bd.BDWorld method)
(ecell4_base.egfrd.EGFRDWorld method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
update_species_attribute() (ecell4_base.core.Model method)
upper() (ecell4_base.core.AABB method)
V
values() (ecell4_base.ode.ODESimulator method)
vertex_at() (ecell4_base.core.Triangle method)
vertices() (ecell4_base.core.Triangle method)
volume() (ecell4_base.core.WorldInterface method)
Voxel (class in ecell4_base.spatiocyte)
voxel() (ecell4_base.spatiocyte.ReactionInfoItem property)
voxel_radius() (ecell4_base.spatiocyte.OffLattice method)
(ecell4_base.spatiocyte.SpatiocyteWorld method)
voxel_volume() (ecell4_base.spatiocyte.SpatiocyteWorld method)
W
whereis() (in module ecell4.datasource)
World (in module ecell4_base.bd)
(in module ecell4_base.egfrd)
(in module ecell4_base.gillespie)
(in module ecell4_base.meso)
(in module ecell4_base.ode)
(in module ecell4_base.spatiocyte)
world() (ecell4_base.bd.BDFactory method)
(ecell4_base.bd.BDSimulator method)
(ecell4_base.egfrd.BDFactory method)
(ecell4_base.egfrd.BDSimulator method)
(ecell4_base.egfrd.EGFRDFactory method)
(ecell4_base.egfrd.EGFRDSimulator method)
(ecell4_base.gillespie.GillespieFactory method)
(ecell4_base.gillespie.GillespieSimulator method)
(ecell4_base.meso.MesoscopicFactory method)
(ecell4_base.meso.MesoscopicSimulator method)
(ecell4_base.ode.ODEFactory method)
(ecell4_base.ode.ODESimulator method)
(ecell4_base.spatiocyte.SpatiocyteFactory method)
(ecell4_base.spatiocyte.SpatiocyteSimulator method)
WorldInterface (class in ecell4_base.core)
wrap_quantity() (in module ecell4.extra.unit)
write_polygon() (in module ecell4_base.core)
X
xroll() (ecell4_base.core.AffineTransformation method)
Y
yroll() (ecell4_base.core.AffineTransformation method)
Z
zroll() (ecell4_base.core.AffineTransformation method)