ecell4_base module

ecell4_base.core submodule

A submodule of ecell4_base

class ecell4_base.core.AABB

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

distance()

is_inside()

lower()

Overloaded function.

surface()

upper()

Overloaded function.
distance()
lower()

Overloaded function.

  1. lower(self: ecell4_base.core.AABB) -> ecell4_base.core.Real3

  2. lower(self: ecell4_base.core.AABB) -> ecell4_base.core.Real3

surface()
upper()

Overloaded function.

  1. upper(self: ecell4_base.core.AABB) -> ecell4_base.core.Real3

  2. upper(self: ecell4_base.core.AABB) -> ecell4_base.core.Real3

class ecell4_base.core.AffineTransformation

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

first()

is_inside()

rescale()

root()

second()

shift()

surface()

third()

translate()

xroll()

yroll()

zroll()

first()
rescale()
root()
second()
shift()
surface()
third()
translate()
xroll()
yroll()
zroll()
class ecell4_base.core.Attriubte

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.Barycentric

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.CSVObserver

Bases: ecell4_base.core.Observer

Methods

filename()

log()

next_time()

num_steps()

reset()

set_formatter()

set_header()

filename()
log()
set_formatter()
set_header()
class ecell4_base.core.Complement

Bases: ecell4_base.core.Shape

Methods

another()

dimension()

dimension_kind

Members:

is_inside()

one()

surface()

another()
one()
surface()
class ecell4_base.core.Cylinder

Bases: ecell4_base.core.Shape

Methods

axis()

center()

dimension()

dimension_kind

Members:

distance()

half_height()

is_inside()

surface()

axis()
center()
distance()
half_height()
surface()
class ecell4_base.core.CylindricalSurface

Bases: ecell4_base.core.Shape

Methods

axis()

center()

dimension()

dimension_kind

Members:

distance()

half_height()

inside()

is_inside()

radius()

axis()
center()
distance()
half_height()
inside()
radius()
class ecell4_base.core.FaceID

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.FixedIntervalCSVObserver

Bases: ecell4_base.core.Observer

Methods

filename()

log()

next_time()

num_steps()

reset()

set_formatter()

set_header()

filename()
log()
set_formatter()
set_header()
class ecell4_base.core.FixedIntervalEvent

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.FixedIntervalHDF5Observer

Bases: ecell4_base.core.Observer

Methods

filename()

Overloaded function.

next_time()

num_steps()

prefix()

reset()

filename()

Overloaded function.

  1. filename(self: ecell4_base.core.FixedIntervalHDF5Observer) -> str

  2. filename(self: ecell4_base.core.FixedIntervalHDF5Observer, arg0: int) -> str

prefix()
class ecell4_base.core.FixedIntervalNumberObserver

Bases: ecell4_base.core.Observer

Methods

data()

next_time()

num_steps()

reset()

save()

targets()

data()
save()
targets()
class ecell4_base.core.FixedIntervalPythonHooker

Bases: ecell4_base.core.Observer

Methods

next_time()

num_steps()

reset()

class ecell4_base.core.FixedIntervalTrackingObserver

Bases: ecell4_base.core.Observer

Methods

data()

next_time()

num_steps()

num_tracers()

reset()

t()

data()
num_tracers()
t()
class ecell4_base.core.FixedIntervalTrajectoryObserver

Bases: ecell4_base.core.Observer

Methods

data()

next_time()

num_steps()

num_tracers()

reset()

t()

data()
num_tracers()
t()
class ecell4_base.core.GSLRandomNumberGenerator

Bases: ecell4_base.core.RandomNumberGenerator

Methods

binomial()

gaussian()

load()

save()

seed()

Overloaded function.

uniform()

Overloaded function.

uniform_int()

class ecell4_base.core.Integer3

Bases: pybind11_builtins.pybind11_object

Attributes
col
layer
row
property col
property layer
property row
class ecell4_base.core.MeshSurface

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

edge_lengths()

filename()

is_inside()

edge_lengths()
filename()
class ecell4_base.core.Model

Bases: pybind11_builtins.pybind11_object

Methods

add_reaction_rule()

add_reaction_rules()

add_species_attribute()

add_species_attributes()

Overloaded function.

apply_species_attributes()

expand()

Overloaded function.

has_reaction_rule()

has_species_attribute()

list_species()

num_reaction_rules()

query_reaction_rules()

Overloaded function.

reaction_rules()

remove_reaction_rule()

remove_species_attribute()

species_attributes()

species_attributes_proceed()

update_species_attribute()

add_reaction_rule()
add_reaction_rules()
add_species_attribute()
add_species_attributes()

Overloaded function.

  1. add_species_attributes(self: ecell4_base.core.Model, arg0: List[ecell4_base.core.Species]) -> None

  2. add_species_attributes(self: ecell4_base.core.Model, arg0: List[Tuple[ecell4_base.core.Species, bool]]) -> None

apply_species_attributes()
expand()

Overloaded function.

  1. expand(self: ecell4_base.core.Model, arg0: List[ecell4_base.core.Species], arg1: int, arg2: Dict[ecell4_base.core.Species, int]) -> ecell4_base.core.Model

  2. expand(self: ecell4_base.core.Model, arg0: List[ecell4_base.core.Species], arg1: int) -> ecell4_base.core.Model

  3. expand(self: ecell4_base.core.Model, arg0: List[ecell4_base.core.Species]) -> ecell4_base.core.Model

has_reaction_rule()
has_species_attribute()
list_species()
num_reaction_rules()
query_reaction_rules()

Overloaded function.

  1. query_reaction_rules(self: ecell4_base.core.Model, arg0: ecell4_base.core.Species) -> List[ecell4_base.core.ReactionRule]

  2. query_reaction_rules(self: ecell4_base.core.Model, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Species) -> List[ecell4_base.core.ReactionRule]

reaction_rules()
remove_reaction_rule()
remove_species_attribute()
species_attributes()
species_attributes_proceed()
update_species_attribute()
class ecell4_base.core.NetfreeModel

Bases: ecell4_base.core.Model

Methods

add_reaction_rule()

add_reaction_rules()

add_species_attribute()

add_species_attributes()

Overloaded function.

apply_species_attributes()

effective()

expand()

Overloaded function.

has_reaction_rule()

has_species_attribute()

list_species()

num_reaction_rules()

query_reaction_rules()

Overloaded function.

reaction_rules()

remove_reaction_rule()

remove_species_attribute()

set_effective()

species_attributes()

species_attributes_proceed()

update_species_attribute()

effective()
set_effective()
class ecell4_base.core.NetworkModel

Bases: ecell4_base.core.Model

Methods

add_reaction_rule()

add_reaction_rules()

add_species_attribute()

add_species_attributes()

Overloaded function.

apply_species_attributes()

expand()

Overloaded function.

has_reaction_rule()

has_species_attribute()

list_species()

num_reaction_rules()

query_reaction_rules()

Overloaded function.

reaction_rules()

remove_reaction_rule()

remove_species_attribute()

species_attributes()

species_attributes_proceed()

update_species_attribute()

class ecell4_base.core.NumberLogger

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.NumberObserver

Bases: ecell4_base.core.Observer

Methods

data()

next_time()

num_steps()

reset()

save()

targets()

data()
save()
targets()
class ecell4_base.core.Observer

Bases: pybind11_builtins.pybind11_object

Methods

next_time()

num_steps()

reset()

next_time()
num_steps()
reset()
class ecell4_base.core.Particle

Bases: pybind11_builtins.pybind11_object

Methods

D()

position()

radius()

species()

D()
position()
radius()
species()
class ecell4_base.core.ParticleID

Bases: pybind11_builtins.pybind11_object

Methods

lot()

serial()

lot()
serial()
class ecell4_base.core.PlanarSurface

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

e0()

e1()

is_inside()

normal()

origin()

e0()
e1()
normal()
origin()
class ecell4_base.core.Polygon

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

is_inside()

reset()

triangles()

reset()
triangles()
ecell4_base.core.Quantity

alias of ecell4_base.core.Quantity_Real

class ecell4_base.core.Quantity_Integer

Bases: pybind11_builtins.pybind11_object

Attributes
magnitude
units
property magnitude
property units
class ecell4_base.core.Quantity_Real

Bases: pybind11_builtins.pybind11_object

Attributes
magnitude
units
property magnitude
property units
class ecell4_base.core.RandomNumberGenerator

Bases: pybind11_builtins.pybind11_object

Methods

binomial()

gaussian()

load()

save()

seed()

Overloaded function.

uniform()

Overloaded function.

uniform_int()

binomial()
gaussian()
load()
save()
seed()

Overloaded function.

  1. seed(self: ecell4_base.core.RandomNumberGenerator) -> None

  2. seed(self: ecell4_base.core.RandomNumberGenerator, arg0: int) -> None

uniform()

Overloaded function.

  1. uniform(self: ecell4_base.core.RandomNumberGenerator, arg0: float, arg1: float) -> float

  2. uniform(self: ecell4_base.core.RandomNumberGenerator, arg0: float, arg1: float) -> float

uniform_int()
class ecell4_base.core.ReactionRule

Bases: pybind11_builtins.pybind11_object

Methods

ReactionRulePolicy

Members:

add_product()

add_reactant()

as_string()

count()

generate()

get_attribute()

get_descriptor()

get_k()

has_attribute()

has_descriptor()

k()

list_attributes()

policy()

products()

reactants()

remove_attribute()

reset_descriptor()

set_attribute()

Overloaded function.

set_descriptor()

set_k()

Overloaded function.

set_policy()

DESTROY = ReactionRulePolicy.DESTROY
IMPLICIT = ReactionRulePolicy.IMPLICIT
class ReactionRulePolicy

Bases: pybind11_builtins.pybind11_object

Members:

STRICT

IMPLICIT

DESTROY

Attributes
name

name(self: handle) -> str

DESTROY = ReactionRulePolicy.DESTROY
IMPLICIT = ReactionRulePolicy.IMPLICIT
STRICT = ReactionRulePolicy.STRICT
property name
STRICT = ReactionRulePolicy.STRICT
add_product()
add_reactant()
as_string()
count()
generate()
get_attribute()
get_descriptor()
get_k()
has_attribute()
has_descriptor()
k()
list_attributes()
policy()
products()
reactants()
remove_attribute()
reset_descriptor()
set_attribute()

Overloaded function.

  1. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: str) -> None

  2. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: str) -> None

  3. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: bool) -> None

  4. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: float) -> None

  5. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: int) -> None

  6. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: ecell4_base.core.Quantity_Real) -> None

  7. set_attribute(self: ecell4_base.core.ReactionRule, arg0: str, arg1: ecell4_base.core.Quantity_Integer) -> None

set_descriptor()
set_k()

Overloaded function.

  1. set_k(self: ecell4_base.core.ReactionRule, arg0: float) -> None

  2. set_k(self: ecell4_base.core.ReactionRule, arg0: ecell4_base.core.Quantity_Real) -> None

set_policy()
class ecell4_base.core.ReactionRuleDescriptor

Bases: pybind11_builtins.pybind11_object

Methods

product_coefficients()

propensity()

reactant_coefficients()

set_product_coefficient()

set_product_coefficients()

set_reactant_coefficient()

set_reactant_coefficients()

product_coefficients()
propensity()
reactant_coefficients()
set_product_coefficient()
set_product_coefficients()
set_reactant_coefficient()
set_reactant_coefficients()
class ecell4_base.core.ReactionRuleDescriptorMassAction

Bases: ecell4_base.core.ReactionRuleDescriptor

Methods

get_k()

k()

product_coefficients()

propensity()

reactant_coefficients()

set_k()

Overloaded function.

set_product_coefficient()

set_product_coefficients()

set_reactant_coefficient()

set_reactant_coefficients()

get_k()
k()
set_k()

Overloaded function.

  1. set_k(self: ecell4_base.core.ReactionRuleDescriptorMassAction, arg0: float) -> None

  2. set_k(self: ecell4_base.core.ReactionRuleDescriptorMassAction, arg0: ecell4_base.core.Quantity_Real) -> None

class ecell4_base.core.ReactionRuleDescriptorPyfunc

Bases: ecell4_base.core.ReactionRuleDescriptor

Methods

as_string()

get()

product_coefficients()

propensity()

reactant_coefficients()

set_name()

set_product_coefficient()

set_product_coefficients()

set_reactant_coefficient()

set_reactant_coefficients()

as_string()
get()
set_name()
class ecell4_base.core.Real3

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.Rod

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

distance()

is_inside()

length()

origin()

radius()

shift()

surface()

distance()
length()
origin()
radius()
shift()
surface()
class ecell4_base.core.RodSurface

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

distance()

is_inside()

length()

origin()

radius()

shift()

distance()
length()
origin()
radius()
shift()
class ecell4_base.core.STLFormat

Bases: pybind11_builtins.pybind11_object

Members:

Ascii

Binary

Attributes
name

name(self: handle) -> str

Ascii = STLFormat.Ascii
Binary = STLFormat.Binary
property name
class ecell4_base.core.Shape

Bases: pybind11_builtins.pybind11_object

Methods

dimension()

dimension_kind

Members:

is_inside()

ONE = dimension_kind.ONE
THREE = dimension_kind.THREE
TWO = dimension_kind.TWO
UNDEF = dimension_kind.UNDEF
dimension()
class dimension_kind

Bases: pybind11_builtins.pybind11_object

Members:

ONE

TWO

THREE

UNDEF

Attributes
name

name(self: handle) -> str

ONE = dimension_kind.ONE
THREE = dimension_kind.THREE
TWO = dimension_kind.TWO
UNDEF = dimension_kind.UNDEF
property name
is_inside()
class ecell4_base.core.Simulator

Bases: pybind11_builtins.pybind11_object

Methods

check_reaction()

dt()

initialize()

next_time()

num_steps()

set_dt()

step()

Overloaded function.

t()

check_reaction()
dt()
initialize()
next_time()
num_steps()
set_dt()
step()

Overloaded function.

  1. step(self: ecell4_base.core.Simulator) -> None

  2. step(self: ecell4_base.core.Simulator, arg0: float) -> bool

t()
class ecell4_base.core.Species

Bases: pybind11_builtins.pybind11_object

Methods

D()

add_unit()

count()

dimension()

get_attribute()

has_attribute()

list_attributes()

location()

radius()

remove_attribute()

serial()

set_attribute()

Overloaded function.

units()

D()
add_unit()
count()
dimension()
get_attribute()
has_attribute()
list_attributes()
location()
radius()
remove_attribute()
serial()
set_attribute()

Overloaded function.

  1. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: str) -> None

  2. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: str) -> None

  3. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: bool) -> None

  4. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: float) -> None

  5. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: int) -> None

  6. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: ecell4_base.core.Quantity_Real) -> None

  7. set_attribute(self: ecell4_base.core.Species, arg0: str, arg1: ecell4_base.core.Quantity_Integer) -> None

units()
class ecell4_base.core.Sphere

Bases: ecell4_base.core.Shape

Methods

center()

dimension()

dimension_kind

Members:

distance()

is_inside()

radius()

surface()

center()
distance()
radius()
surface()
class ecell4_base.core.SphericalSurface

Bases: ecell4_base.core.Shape

Methods

center()

dimension()

dimension_kind

Members:

distance()

inside()

is_inside()

radius()

center()
distance()
inside()
radius()
class ecell4_base.core.Surface

Bases: ecell4_base.core.Shape

Methods

dimension()

dimension_kind

Members:

is_inside()

root()

root()
class ecell4_base.core.TimeoutObserver

Bases: ecell4_base.core.Observer

Methods

accumulation()

duration()

interval()

next_time()

num_steps()

reset()

accumulation()
duration()
interval()
class ecell4_base.core.TimingEvent

Bases: pybind11_builtins.pybind11_object

class ecell4_base.core.TimingNumberObserver

Bases: ecell4_base.core.Observer

Methods

data()

next_time()

num_steps()

reset()

save()

targets()

data()
save()
targets()
class ecell4_base.core.TimingTrajectoryObserver

Bases: ecell4_base.core.Observer

Methods

data()

next_time()

num_steps()

num_tracers()

reset()

t()

data()
num_tracers()
t()
class ecell4_base.core.Triangle

Bases: ecell4_base.core.Shape

Methods

area()

dimension()

dimension_kind

Members:

is_inside()

normal()

vertex_at()

vertices()

area()
normal()
vertex_at()
vertices()
class ecell4_base.core.Union

Bases: ecell4_base.core.Shape

Methods

another()

dimension()

dimension_kind

Members:

is_inside()

one()

surface()

another()
one()
surface()
class ecell4_base.core.UnitSpecies

Bases: pybind11_builtins.pybind11_object

Methods

add_site()

clear()

deserialize()

get_site()

has_site()

name()

serial()

set_name()

sites()

add_site()
clear()
deserialize()
get_site()
has_site()
name()
serial()
set_name()
sites()
class ecell4_base.core.WorldInterface

Bases: pybind11_builtins.pybind11_object

Methods

edge_lengths()

get_particle()

get_value()

get_value_exact()

has_particle()

has_species()

list_particles()

Overloaded function.

list_particles_exact()

list_species()

load()

num_molecules()

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

save()

set_t()

t()

volume()

edge_lengths()
get_particle()
get_value()
get_value_exact()
has_particle()
has_species()
list_particles()

Overloaded function.

  1. list_particles(self: ecell4_base.core.WorldInterface) -> List[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle]]

  2. list_particles(self: ecell4_base.core.WorldInterface, arg0: ecell4_base.core.Species) -> List[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle]]

list_particles_exact()
list_species()
load()
num_molecules()
num_molecules_exact()
num_particles()

Overloaded function.

  1. num_particles(self: ecell4_base.core.WorldInterface) -> int

  2. num_particles(self: ecell4_base.core.WorldInterface, arg0: ecell4_base.core.Species) -> int

num_particles_exact()
save()
set_t()
t()
volume()
ecell4_base.core.cbrt()
ecell4_base.core.count_species_matches()
ecell4_base.core.create_binding_reaction_rule()
ecell4_base.core.create_degradation_reaction_rule()
ecell4_base.core.create_synthesis_reaction_rule()
ecell4_base.core.create_unbinding_reaction_rule()
ecell4_base.core.create_unimolecular_reaction_rule()
ecell4_base.core.create_x_plane()
ecell4_base.core.create_y_plane()
ecell4_base.core.create_z_plane()
ecell4_base.core.cross_product()
ecell4_base.core.dot_product()

Overloaded function.

  1. dot_product(arg0: ecell4_base.core.Real3, arg1: ecell4_base.core.Real3) -> float

  2. dot_product(arg0: ecell4_base.core.Integer3, arg1: ecell4_base.core.Integer3) -> int

ecell4_base.core.format_species()
ecell4_base.core.get_dimension_from_model()
ecell4_base.core.get_stoichiometry()
ecell4_base.core.integer3_abs()
ecell4_base.core.integer3_add()
ecell4_base.core.integer3_dot_product()
ecell4_base.core.integer3_length()
ecell4_base.core.integer3_length_sq()
ecell4_base.core.integer3_multiply()
ecell4_base.core.integer3_subtract()
ecell4_base.core.length()

Overloaded function.

  1. length(arg0: ecell4_base.core.Real3) -> float

  2. length(arg0: ecell4_base.core.Integer3) -> float

ecell4_base.core.length_sq()

Overloaded function.

  1. length_sq(arg0: ecell4_base.core.Real3) -> float

  2. length_sq(arg0: ecell4_base.core.Integer3) -> int

ecell4_base.core.load_version_information()
ecell4_base.core.ones()
ecell4_base.core.read_polygon()
ecell4_base.core.real3_abs()
ecell4_base.core.real3_add()
ecell4_base.core.real3_divide()
ecell4_base.core.real3_dot_product()
ecell4_base.core.real3_length()
ecell4_base.core.real3_length_sq()
ecell4_base.core.real3_multiply()
ecell4_base.core.real3_subtract()
ecell4_base.core.unitx()
ecell4_base.core.unity()
ecell4_base.core.unitz()
ecell4_base.core.write_polygon()

ecell4_base.bd submodule

A submodule of ecell4_base

class ecell4_base.bd.BDFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.bd.BDFactory, world: ecell4::bd::BDWorld) -> ecell4::bd::BDSimulator

  2. simulator(self: ecell4_base.bd.BDFactory, world: ecell4::bd::BDWorld, model: ecell4_base.core.Model) -> ecell4::bd::BDSimulator

world()

Overloaded function.

  1. world(self: ecell4_base.bd.BDFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd66a02308>) -> ecell4::bd::BDWorld

  2. world(self: ecell4_base.bd.BDFactory, volume: float) -> ecell4::bd::BDWorld

  3. world(self: ecell4_base.bd.BDFactory, filename: str) -> ecell4::bd::BDWorld

  4. world(self: ecell4_base.bd.BDFactory, model: ecell4_base.core.Model) -> ecell4::bd::BDWorld

class ecell4_base.bd.BDSimulator

Bases: ecell4_base.core.Simulator

Methods

check_reaction()

dt()

initialize()

last_reactions()

model()

next_time()

num_steps()

run()

Overloaded function.

set_dt()

set_t()

step()

Overloaded function.

t()

world()

last_reactions()
model()
run()

Overloaded function.

  1. run(self: ecell4_base.bd.BDSimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.bd.BDSimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.bd.BDSimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_t()
world()
class ecell4_base.bd.BDWorld

Bases: ecell4_base.core.WorldInterface

Methods

add_molecules()

Overloaded function.

apply_boundary()

bind_to()

distance()

distance_sq()

edge_lengths()

get_particle()

get_value()

get_value_exact()

has_particle()

has_species()

list_particles()

Overloaded function.

list_particles_exact()

list_particles_within_radius()

Overloaded function.

list_species()

load()

new_particle()

Overloaded function.

num_molecules()

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

periodic_transpose()

remove_molecules()

remove_particle()

rng()

save()

set_t()

t()

update_particle()

volume()

add_molecules()

Overloaded function.

  1. add_molecules(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Species, arg1: int) -> None

  2. add_molecules(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Shape) -> None

apply_boundary()
bind_to()
distance()
distance_sq()
list_particles_within_radius()

Overloaded function.

  1. list_particles_within_radius(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Real3, arg1: float) -> List[Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], float]]

  2. list_particles_within_radius(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Real3, arg1: float, arg2: ecell4_base.core.ParticleID) -> List[Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], float]]

  3. list_particles_within_radius(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Real3, arg1: float, arg2: ecell4_base.core.ParticleID, arg3: ecell4_base.core.ParticleID) -> List[Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], float]]

new_particle()

Overloaded function.

  1. new_particle(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Particle) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

  2. new_particle(self: ecell4_base.bd.BDWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Real3) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

periodic_transpose()
remove_molecules()
remove_particle()
rng()
update_particle()
ecell4_base.bd.Factory

alias of ecell4_base.bd.BDFactory

class ecell4_base.bd.ReactionInfo

Bases: pybind11_builtins.pybind11_object

Methods

products()

reactants()

t()

products()
reactants()
t()
ecell4_base.bd.Simulator

alias of ecell4_base.bd.BDSimulator

ecell4_base.bd.World

alias of ecell4_base.bd.BDWorld

ecell4_base.egfrd submodule

A submodule of ecell4_base

class ecell4_base.egfrd.BDFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.egfrd.BDFactory, world: ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >) -> ecell4_base.egfrd.BDSimulator

  2. simulator(self: ecell4_base.egfrd.BDFactory, world: ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >, model: ecell4_base.core.Model) -> ecell4_base.egfrd.BDSimulator

world()

Overloaded function.

  1. world(self: ecell4_base.egfrd.BDFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd66a02618>) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

  2. world(self: ecell4_base.egfrd.BDFactory, volume: float) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

  3. world(self: ecell4_base.egfrd.BDFactory, filename: str) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

  4. world(self: ecell4_base.egfrd.BDFactory, model: ecell4_base.core.Model) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

class ecell4_base.egfrd.BDSimulator

Bases: ecell4_base.core.Simulator

Methods

add_potential()

Overloaded function.

check_reaction()

dt()

dt_factor()

initialize()

last_reactions()

model()

next_time()

num_steps()

run()

Overloaded function.

set_dt()

set_t()

step()

Overloaded function.

t()

world()

add_potential()

Overloaded function.

  1. add_potential(self: ecell4_base.egfrd.BDSimulator, arg0: ecell4_base.core.Species, arg1: float) -> None

  2. add_potential(self: ecell4_base.egfrd.BDSimulator, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Shape) -> None

  3. add_potential(self: ecell4_base.egfrd.BDSimulator, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Shape, arg2: float) -> None

dt_factor()
last_reactions()
model()
run()

Overloaded function.

  1. run(self: ecell4_base.egfrd.BDSimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.egfrd.BDSimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.egfrd.BDSimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_t()
world()
class ecell4_base.egfrd.EGFRDFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.egfrd.EGFRDFactory, world: ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >) -> ecell4::egfrd::EGFRDSimulator<ecell4::egfrd::EGFRDSimulatorTraitsBase<ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> > > >

  2. simulator(self: ecell4_base.egfrd.EGFRDFactory, world: ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >, model: ecell4_base.core.Model) -> ecell4::egfrd::EGFRDSimulator<ecell4::egfrd::EGFRDSimulatorTraitsBase<ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> > > >

world()

Overloaded function.

  1. world(self: ecell4_base.egfrd.EGFRDFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd66a026c0>) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

  2. world(self: ecell4_base.egfrd.EGFRDFactory, volume: float) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

  3. world(self: ecell4_base.egfrd.EGFRDFactory, filename: str) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

  4. world(self: ecell4_base.egfrd.EGFRDFactory, model: ecell4_base.core.Model) -> ecell4::egfrd::World<ecell4::egfrd::CyclicWorldTraits<double> >

class ecell4_base.egfrd.EGFRDSimulator

Bases: ecell4_base.core.Simulator

Methods

check_reaction()

dt()

initialize()

last_reactions()

model()

next_time()

num_steps()

run()

Overloaded function.

set_dt()

set_paranoiac()

set_t()

step()

Overloaded function.

t()

world()

last_reactions()
model()
run()

Overloaded function.

  1. run(self: ecell4_base.egfrd.EGFRDSimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.egfrd.EGFRDSimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.egfrd.EGFRDSimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_paranoiac()
set_t()
world()
class ecell4_base.egfrd.EGFRDWorld

Bases: ecell4_base.core.WorldInterface

Methods

add_molecules()

Overloaded function.

apply_boundary()

bind_to()

distance()

edge_lengths()

get_particle()

get_value()

get_value_exact()

has_particle()

has_species()

list_particles()

Overloaded function.

list_particles_exact()

list_particles_within_radius()

Overloaded function.

list_species()

load()

matrix_sizes()

new_particle()

Overloaded function.

num_molecules()

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

remove_molecules()

remove_particle()

rng()

save()

set_t()

set_value()

t()

update_particle()

volume()

add_molecules()

Overloaded function.

  1. add_molecules(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Species, arg1: int) -> None

  2. add_molecules(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Shape) -> None

apply_boundary()
bind_to()
distance()
list_particles_within_radius()

Overloaded function.

  1. list_particles_within_radius(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Real3, arg1: float) -> List[Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], float]]

  2. list_particles_within_radius(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Real3, arg1: float, arg2: ecell4_base.core.ParticleID) -> List[Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], float]]

  3. list_particles_within_radius(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Real3, arg1: float, arg2: ecell4_base.core.ParticleID, arg3: ecell4_base.core.ParticleID) -> List[Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], float]]

matrix_sizes()
new_particle()

Overloaded function.

  1. new_particle(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Particle) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

  2. new_particle(self: ecell4_base.egfrd.EGFRDWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Real3) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

remove_molecules()
remove_particle()
rng()
set_value()
update_particle()
ecell4_base.egfrd.Factory

alias of ecell4_base.egfrd.EGFRDFactory

class ecell4_base.egfrd.ReactionInfo

Bases: pybind11_builtins.pybind11_object

Methods

products()

reactants()

t()

products()
reactants()
t()
ecell4_base.egfrd.Simulator

alias of ecell4_base.egfrd.EGFRDSimulator

ecell4_base.egfrd.World

alias of ecell4_base.egfrd.EGFRDWorld

ecell4_base.gillespie submodule

A submodule of ecell4_base

ecell4_base.gillespie.Factory

alias of ecell4_base.gillespie.GillespieFactory

class ecell4_base.gillespie.GillespieFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.gillespie.GillespieFactory, world: ecell4::gillespie::GillespieWorld) -> ecell4::gillespie::GillespieSimulator

  2. simulator(self: ecell4_base.gillespie.GillespieFactory, world: ecell4::gillespie::GillespieWorld, model: ecell4_base.core.Model) -> ecell4::gillespie::GillespieSimulator

world()

Overloaded function.

  1. world(self: ecell4_base.gillespie.GillespieFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd66a02848>) -> ecell4::gillespie::GillespieWorld

  2. world(self: ecell4_base.gillespie.GillespieFactory, volume: float) -> ecell4::gillespie::GillespieWorld

  3. world(self: ecell4_base.gillespie.GillespieFactory, filename: str) -> ecell4::gillespie::GillespieWorld

  4. world(self: ecell4_base.gillespie.GillespieFactory, model: ecell4_base.core.Model) -> ecell4::gillespie::GillespieWorld

class ecell4_base.gillespie.GillespieSimulator

Bases: ecell4_base.core.Simulator

Methods

check_reaction()

dt()

initialize()

last_reactions()

model()

next_time()

num_steps()

run()

Overloaded function.

set_dt()

set_t()

step()

Overloaded function.

t()

world()

last_reactions()
model()
run()

Overloaded function.

  1. run(self: ecell4_base.gillespie.GillespieSimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.gillespie.GillespieSimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.gillespie.GillespieSimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_t()
world()
class ecell4_base.gillespie.GillespieWorld

Bases: ecell4_base.core.WorldInterface

Methods

add_molecules()

Overloaded function.

bind_to()

edge_lengths()

get_particle()

get_value()

get_value_exact()

has_particle()

has_species()

list_particles()

Overloaded function.

list_particles_exact()

list_species()

load()

new_particle()

Overloaded function.

num_molecules()

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

remove_molecules()

rng()

save()

set_t()

set_value()

t()

volume()

add_molecules()

Overloaded function.

  1. add_molecules(self: ecell4_base.gillespie.GillespieWorld, arg0: ecell4_base.core.Species, arg1: int) -> None

  2. add_molecules(self: ecell4_base.gillespie.GillespieWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Shape) -> None

bind_to()
new_particle()

Overloaded function.

  1. new_particle(self: ecell4_base.gillespie.GillespieWorld, arg0: ecell4_base.core.Particle) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

  2. new_particle(self: ecell4_base.gillespie.GillespieWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Real3) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

remove_molecules()
rng()
set_value()
class ecell4_base.gillespie.ReactionInfo

Bases: pybind11_builtins.pybind11_object

Methods

products()

reactants()

t()

products()
reactants()
t()
ecell4_base.gillespie.Simulator

alias of ecell4_base.gillespie.GillespieSimulator

ecell4_base.gillespie.World

alias of ecell4_base.gillespie.GillespieWorld

ecell4_base.meso submodule

A submodule of ecell4_base

ecell4_base.meso.Factory

alias of ecell4_base.meso.MesoscopicFactory

class ecell4_base.meso.MesoscopicFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.meso.MesoscopicFactory, world: ecell4::meso::MesoscopicWorld) -> ecell4::meso::MesoscopicSimulator

  2. simulator(self: ecell4_base.meso.MesoscopicFactory, world: ecell4::meso::MesoscopicWorld, model: ecell4_base.core.Model) -> ecell4::meso::MesoscopicSimulator

world()

Overloaded function.

  1. world(self: ecell4_base.meso.MesoscopicFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd66a029d0>) -> ecell4::meso::MesoscopicWorld

  2. world(self: ecell4_base.meso.MesoscopicFactory, volume: float) -> ecell4::meso::MesoscopicWorld

  3. world(self: ecell4_base.meso.MesoscopicFactory, filename: str) -> ecell4::meso::MesoscopicWorld

  4. world(self: ecell4_base.meso.MesoscopicFactory, model: ecell4_base.core.Model) -> ecell4::meso::MesoscopicWorld

class ecell4_base.meso.MesoscopicSimulator

Bases: ecell4_base.core.Simulator

Methods

check_reaction()

dt()

initialize()

last_reactions()

model()

next_time()

num_steps()

run()

Overloaded function.

set_dt()

set_t()

step()

Overloaded function.

t()

world()

last_reactions()
model()
run()

Overloaded function.

  1. run(self: ecell4_base.meso.MesoscopicSimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.meso.MesoscopicSimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.meso.MesoscopicSimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_t()
world()
class ecell4_base.meso.MesoscopicWorld

Bases: ecell4_base.core.WorldInterface

Methods

add_molecules()

Overloaded function.

add_structure()

bind_to()

check_structure()

coord2global()

edge_lengths()

get_data()

get_occupancy()

Overloaded function.

get_particle()

get_value()

get_value_exact()

get_volume()

global2coord()

has_particle()

has_species()

has_structure()

list_coordinates()

list_coordinates_exact()

list_particles()

Overloaded function.

list_particles_exact()

list_species()

load()

matrix_sizes()

new_particle()

Overloaded function.

num_molecules()

Overloaded function.

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

num_subvolumes()

Overloaded function.

on_structure()

position2coordinate()

position2global()

remove_molecules()

Overloaded function.

rng()

save()

set_t()

set_value()

subvolume()

subvolume_edge_lengths()

t()

volume()

add_molecules()

Overloaded function.

  1. add_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int) -> None

  2. add_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: int) -> None

  3. add_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Integer3) -> None

  4. add_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Shape) -> None

add_structure()
bind_to()
check_structure()
coord2global()
get_data()
get_occupancy()

Overloaded function.

  1. get_occupancy(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int) -> float

  2. get_occupancy(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Integer3) -> float

get_volume()
global2coord()
has_structure()
list_coordinates()
list_coordinates_exact()
matrix_sizes()
new_particle()

Overloaded function.

  1. new_particle(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Particle) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

  2. new_particle(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Real3) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

num_molecules()

Overloaded function.

  1. num_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species) -> int

  2. num_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int) -> int

  3. num_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Integer3) -> int

num_subvolumes()

Overloaded function.

  1. num_subvolumes(self: ecell4_base.meso.MesoscopicWorld) -> int

  2. num_subvolumes(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species) -> int

on_structure()
position2coordinate()
position2global()
remove_molecules()

Overloaded function.

  1. remove_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int) -> None

  2. remove_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Integer3) -> None

  3. remove_molecules(self: ecell4_base.meso.MesoscopicWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: int) -> None

rng()
set_value()
subvolume()
subvolume_edge_lengths()
class ecell4_base.meso.ReactionInfo

Bases: pybind11_builtins.pybind11_object

Methods

coordinate()

products()

reactants()

t()

coordinate()
products()
reactants()
t()
ecell4_base.meso.Simulator

alias of ecell4_base.meso.MesoscopicSimulator

ecell4_base.meso.World

alias of ecell4_base.meso.MesoscopicWorld

ecell4_base.ode submodule

A submodule of ecell4_base

ecell4_base.ode.Factory

alias of ecell4_base.ode.ODEFactory

class ecell4_base.ode.ODEFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.ode.ODEFactory, world: ecell4::ode::ODEWorld) -> ecell4::ode::ODESimulator

  2. simulator(self: ecell4_base.ode.ODEFactory, world: ecell4::ode::ODEWorld, model: ecell4_base.core.Model) -> ecell4::ode::ODESimulator

world()

Overloaded function.

  1. world(self: ecell4_base.ode.ODEFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd66a02d88>) -> ecell4::ode::ODEWorld

  2. world(self: ecell4_base.ode.ODEFactory, volume: float) -> ecell4::ode::ODEWorld

  3. world(self: ecell4_base.ode.ODEFactory, filename: str) -> ecell4::ode::ODEWorld

  4. world(self: ecell4_base.ode.ODEFactory, model: ecell4_base.core.Model) -> ecell4::ode::ODEWorld

class ecell4_base.ode.ODESimulator

Bases: ecell4_base.core.Simulator

Methods

absolute_tolerance()

check_reaction()

derivatives()

dt()

elasticity()

fluxes()

initialize()

jacobian()

maximum_step_interval()

model()

next_time()

num_steps()

relative_tolerance()

run()

Overloaded function.

set_absolute_tolerance()

set_dt()

set_maximum_step_interval()

set_relative_tolerance()

set_t()

step()

Overloaded function.

stoichiometry()

t()

values()

world()

absolute_tolerance()
derivatives()
elasticity()
fluxes()
jacobian()
maximum_step_interval()
model()
relative_tolerance()
run()

Overloaded function.

  1. run(self: ecell4_base.ode.ODESimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.ode.ODESimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.ode.ODESimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_absolute_tolerance()
set_maximum_step_interval()
set_relative_tolerance()
set_t()
stoichiometry()
values()
world()
class ecell4_base.ode.ODESolverType

Bases: pybind11_builtins.pybind11_object

Members:

RUNGE_KUTTA_CASH_KARP54

ROSENBROCK4_CONTROLLER

EULER

Attributes
name

name(self: handle) -> str

EULER = ODESolverType.EULER
ROSENBROCK4_CONTROLLER = ODESolverType.ROSENBROCK4_CONTROLLER
RUNGE_KUTTA_CASH_KARP54 = ODESolverType.RUNGE_KUTTA_CASH_KARP54
property name
class ecell4_base.ode.ODEWorld

Bases: ecell4_base.core.WorldInterface

Methods

add_molecules()

Overloaded function.

bind_to()

edge_lengths()

evaluate()

Overloaded function.

get_particle()

get_value()

get_value_exact()

get_values()

has_particle()

has_species()

list_particles()

Overloaded function.

list_particles_exact()

list_species()

load()

new_particle()

Overloaded function.

num_molecules()

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

release_species()

remove_molecules()

reserve_species()

save()

set_t()

set_value()

set_volume()

t()

volume()

add_molecules()

Overloaded function.

  1. add_molecules(self: ecell4_base.ode.ODEWorld, arg0: ecell4_base.core.Species, arg1: float) -> None

  2. add_molecules(self: ecell4_base.ode.ODEWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Shape) -> None

bind_to()
evaluate()

Overloaded function.

  1. evaluate(self: ecell4_base.ode.ODEWorld, arg0: List[ecell4_base.core.ReactionRule]) -> List[float]

  2. evaluate(self: ecell4_base.ode.ODEWorld, arg0: ecell4_base.core.ReactionRule) -> float

get_values()
new_particle()

Overloaded function.

  1. new_particle(self: ecell4_base.ode.ODEWorld, arg0: ecell4_base.core.Particle) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

  2. new_particle(self: ecell4_base.ode.ODEWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Real3) -> Tuple[Tuple[ecell4_base.core.ParticleID, ecell4_base.core.Particle], bool]

release_species()
remove_molecules()
reserve_species()
set_value()
set_volume()
ecell4_base.ode.Simulator

alias of ecell4_base.ode.ODESimulator

ecell4_base.ode.World

alias of ecell4_base.ode.ODEWorld

ecell4_base.spatiocyte submodule

A submodule of ecell4_base

ecell4_base.spatiocyte.Factory

alias of ecell4_base.spatiocyte.SpatiocyteFactory

class ecell4_base.spatiocyte.OffLattice

Bases: pybind11_builtins.pybind11_object

Methods

adjoining_pairs()

positions()

voxel_radius()

adjoining_pairs()
positions()
voxel_radius()
class ecell4_base.spatiocyte.ReactionInfo

Bases: pybind11_builtins.pybind11_object

Methods

products()

reactants()

t()

products()
reactants()
t()
class ecell4_base.spatiocyte.ReactionInfoItem

Bases: pybind11_builtins.pybind11_object

Attributes
pid
species
voxel
property pid
property species
property voxel
ecell4_base.spatiocyte.Simulator

alias of ecell4_base.spatiocyte.SpatiocyteSimulator

class ecell4_base.spatiocyte.SpatiocyteFactory

Bases: pybind11_builtins.pybind11_object

Methods

rng()

simulator()

Overloaded function.

world()

Overloaded function.
rng()
simulator()

Overloaded function.

  1. simulator(self: ecell4_base.spatiocyte.SpatiocyteFactory, world: ecell4::spatiocyte::SpatiocyteWorld) -> ecell4::spatiocyte::SpatiocyteSimulator

  2. simulator(self: ecell4_base.spatiocyte.SpatiocyteFactory, world: ecell4::spatiocyte::SpatiocyteWorld, model: ecell4_base.core.Model) -> ecell4::spatiocyte::SpatiocyteSimulator

world()

Overloaded function.

  1. world(self: ecell4_base.spatiocyte.SpatiocyteFactory, edge_lengths: ecell4_base.core.Real3 = <ecell4_base.core.Real3 object at 0x7efd6699e110>) -> ecell4::spatiocyte::SpatiocyteWorld

  2. world(self: ecell4_base.spatiocyte.SpatiocyteFactory, volume: float) -> ecell4::spatiocyte::SpatiocyteWorld

  3. world(self: ecell4_base.spatiocyte.SpatiocyteFactory, filename: str) -> ecell4::spatiocyte::SpatiocyteWorld

  4. world(self: ecell4_base.spatiocyte.SpatiocyteFactory, model: ecell4_base.core.Model) -> ecell4::spatiocyte::SpatiocyteWorld

class ecell4_base.spatiocyte.SpatiocyteSimulator

Bases: ecell4_base.core.Simulator

Methods

check_reaction()

dt()

initialize()

last_reactions()

model()

next_time()

num_steps()

run()

Overloaded function.

set_dt()

set_t()

step()

Overloaded function.

t()

world()

last_reactions()
model()
run()

Overloaded function.

  1. run(self: ecell4_base.spatiocyte.SpatiocyteSimulator, duration: float, is_dirty: bool = True) -> None

  2. run(self: ecell4_base.spatiocyte.SpatiocyteSimulator, duration: float, observer: ecell4_base.core.Observer, is_dirty: bool = True) -> None

  3. run(self: ecell4_base.spatiocyte.SpatiocyteSimulator, duration: float, observers: List[ecell4_base.core.Observer], is_dirty: bool = True) -> None

set_t()
world()
class ecell4_base.spatiocyte.SpatiocyteWorld

Bases: ecell4_base.core.WorldInterface

Methods

add_molecules()

Overloaded function.

add_offlattice()

add_structure()

bind_to()

calculate_hcp_lengths()

calculate_shape()

calculate_volume()

calculate_voxel_volume()

edge_lengths()

get_particle()

get_species_at()

get_value()

get_value_exact()

get_volume()

get_voxel()

get_voxel_at()

get_voxel_near_by()

Deprecated since version 3.0.

get_voxel_nearby()

has_particle()

has_particle_at()

has_species()

has_voxel()

Deprecated since version 3.0.

list_neighbors()

list_non_structure_particles()

list_particles()

Overloaded function.

list_particles_exact()

list_species()

list_structure_particles()

load()

new_particle()

Overloaded function.

new_voxel()

new_voxel_structure()

num_molecules()

num_molecules_exact()

num_particles()

Overloaded function.

num_particles_exact()

remove_molecules()

remove_particle()

remove_voxel()

Deprecated since version 3.0.

rng()

save()

set_t()

set_value()

shape()

size()

t()

update_particle()

volume()

voxel_radius()

voxel_volume()

add_molecules()

Overloaded function.

  1. add_molecules(self: ecell4_base.spatiocyte.SpatiocyteWorld, arg0: ecell4_base.core.Species, arg1: int) -> bool

  2. add_molecules(self: ecell4_base.spatiocyte.SpatiocyteWorld, arg0: ecell4_base.core.Species, arg1: int, arg2: ecell4_base.core.Shape) -> bool

add_offlattice()
add_structure()
bind_to()
static calculate_hcp_lengths()
static calculate_shape()
static calculate_volume()
static calculate_voxel_volume()
get_species_at()
get_volume()
get_voxel()
get_voxel_at()
get_voxel_near_by()

Deprecated since version 3.0: Use get_voxel_nearby() instead.

get_voxel_nearby()
has_particle_at()
has_voxel()

Deprecated since version 3.0: Use has_particle() instead.

list_neighbors()
list_non_structure_particles()
list_structure_particles()
new_particle()

Overloaded function.

  1. new_particle(self: ecell4_base.spatiocyte.SpatiocyteWorld, arg0: ecell4_base.core.Particle) -> Optional[ecell4_base.core.ParticleID]

  2. new_particle(self: ecell4_base.spatiocyte.SpatiocyteWorld, arg0: ecell4_base.core.Species, arg1: ecell4_base.core.Real3) -> Optional[ecell4_base.core.ParticleID]

  3. new_particle(self: ecell4_base.spatiocyte.SpatiocyteWorld, arg0: ecell4_base.core.Species, arg1: ecell4::spatiocyte::Voxel) -> Optional[ecell4_base.core.ParticleID]

new_voxel()
new_voxel_structure()
remove_molecules()
remove_particle()
remove_voxel()

Deprecated since version 3.0: Use remove_particle() instead.

rng()
set_value()
shape()
size()
update_particle()
voxel_radius()
voxel_volume()
class ecell4_base.spatiocyte.Voxel

Bases: pybind11_builtins.pybind11_object

Methods

position()

position()
ecell4_base.spatiocyte.World

alias of ecell4_base.spatiocyte.SpatiocyteWorld

ecell4_base.spatiocyte.create_spatiocyte_world_cell_list_impl()
ecell4_base.spatiocyte.create_spatiocyte_world_square_offlattice_impl()
ecell4_base.spatiocyte.create_spatiocyte_world_vector_impl()
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