Tutorial 6 (World Advanced)

This is a tutorial for E-Cell4.



In [1]:

    
from ecell4.core import *
from ecell4.gillespie import GillespieWorld
from ecell4.ode import ODEWorld
from ecell4.lattice import LatticeWorld
from ecell4.bd import BDWorld

edge_lengths = Real3(1, 2, 3)



In [2]:

    
m = NetworkModel()
m.add_species_attribute(Species("A", "0.0025", "1"))

ParticleSpace interfaces:



In [3]:

    
w = BDWorld(edge_lengths)
# w = LatticeWorld(edge_lengths)
w.bind_to(m)

Create a new particle. new_particle returns a pair of ParticleID and Particle with if the creation is succeeded or not.



In [4]:

    
((pid, p), is_succeeded) = w.new_particle(Species("A"), Real3(0.5, 0.5, 0.5))



In [5]:

    
print(pid, p, is_succeeded)
print(w.num_molecules(Species("A")))









    



<ecell4.core.ParticleID object at 0x7fcc5bb5c450> <ecell4.core.Particle object at 0x7fcc5bb5c498> True
1

ParticleID is a pair of Integers named serial and lot. Particle consists of species, position, radius, D.



In [6]:

    
print(pid.serial(), pid.lot())
print(p.species().serial(), tuple(p.position()), p.radius(), p.D())









    



1 0
A (0.5, 0.5, 0.5) 0.0025 1.0

ParticleSpace has interfaces to check if the ParticleID exists (has_particle), to list all particles belonging to the Species (list_particles), and to get Particle assigned to the given ParticleID (get_particle).



In [7]:

    
print(w.has_particle(pid))
print(w.list_particles(Species("A")))
print(w.get_particle(pid))









    



True
[(<ecell4.core.ParticleID object at 0x7fcc5bb5c4f8>, <ecell4.core.Particle object at 0x7fcc5bb5c540>)]
(<ecell4.core.ParticleID object at 0x7fcc5bb5c4f8>, <ecell4.core.Particle object at 0x7fcc5bb5c510>)

To move a Particle to the new position, use update_particle. update_particle tries to replace the Particle with given one.



In [8]:

    
w.update_particle(pid, Particle(p.species(), Real3(0.5, 1.5, 2.5), p.radius(), p.D()))
_, newp = w.get_particle(pid)
print(tuple(newp.position()), w.num_molecules(Species("A")))









    



(0.5, 1.5, 2.5) 1

You can remove a Particle by remove_particle.



In [9]:

    
w.remove_particle(pid)
print(w.has_particle(pid))









    



False



In [10]:

    
del w

LatticeSpace interfaces:



In [11]:

    
w = LatticeWorld(edge_lengths)
w.bind_to(m)

LatticeSpace has interfaces to give essential information about it.



In [12]:

    
print(w.voxel_radius(), w.row_size(), w.col_size(), w.layer_size())









    



0.01 150 61 115

Positions in LatticeSpace is represented as a single Integer named coordinate, which is corresponding to Real3 (position) in ParticleSpace. coordinate2position and position2coordinate give the way to convert between them.



In [13]:

    
coord = w.position2coordinate(Real3(0.5, 0.5, 0.5))
pos = w.coordinate2position(coord)
new_coord = w.position2coordinate(pos)

print(coord, tuple(pos))
print(new_coord, tuple(w.coordinate2position(new_coord)))
print(w.position2coordinate(Real3(0.5, 1.5, 2.5)))









    



270025 (0.5062278801751902, 0.5080682368868706, 0.5)
270025 (0.5062278801751902, 0.5080682368868706, 0.5)
791675

Interfaces similar to ParticleSpace are available in LatticeSpace.



In [14]:

    
((pid, v), is_succeeded) = w.new_voxel(Species("A"), coord)



In [15]:

    
print(pid, v, is_succeeded)
print(w.num_molecules(Species("A")))









    



<ecell4.core.ParticleID object at 0x7fcc5bb5c5a0> <ecell4.core.Voxel object at 0x7fcc5bb5c678> True
1



In [16]:

    
print(v.species().serial(), v.coordinate(), v.radius(), v.D())









    



A 270025 0.0025 1.0



In [17]:

    
print(w.has_particle(pid))
print(w.list_voxels(Species("A")))
print(w.get_voxel(pid))









    



True
[(<ecell4.core.ParticleID object at 0x7fcc5bb5c588>, <ecell4.core.Voxel object at 0x7fcc5bb5c690>)]
(<ecell4.core.ParticleID object at 0x7fcc5bb5c588>, <ecell4.core.Voxel object at 0x7fcc5bb5c450>)



In [18]:

    
w.update_voxel(pid, Voxel(v.species(), 791525, v.radius(), v.D()))
_, newv = w.get_voxel(pid)
print(newv.coordinate(), w.num_molecules(Species("A")))



In [19]:

    
w.remove_voxel(pid)
print(w.has_voxel(pid))









    



False

RandomNumberGenerator interfaces:



In [20]:

    
rng1, rng2 = GSLRandomNumberGenerator(), GSLRandomNumberGenerator()
rng1.seed(0)
rng2.seed(0)
print(rng1.uniform(0, 1), rng2.uniform(0, 1))
print(rng1.uniform_int(0, 100), rng2.uniform_int(0, 100))
print(rng1.gaussian(0.0, 1.0), rng2.gaussian(0.0, 1.0))









    



0.999741748906672 0.999741748906672
16 16
1.0 1.0

GillespieWorld, LatticeWorld and BDWorld can be constructed with a GSLRandomNumberGenerator. rng() returns a shared object of RandomNumberGenerator. In below, w.rng() and rng1 point the same RandomNumberGenerator.



In [21]:

    
w = GillespieWorld(Real3(1, 1, 1), rng1)
# w = BDWorld(Real3(1, 1, 1), rng1)
# w = LatticeWorld(Real3(1, 1, 1), 0.05, rng1) # The second argument is voxel_radius.



In [22]:

    
print(w.rng().uniform(0, 1), rng2.uniform(0, 1), rng1.uniform(0, 1))









    



0.23165654274635017 0.23165654274635017 0.48497361433692276



In [23]:

    
del rng1, rng2
print(w.rng().uniform(0, 1))
del w









    



0.9574769565369934



In [23]: