This is a tutorial for E-Cell4. Here, we explain the basics of World classes. In E-Cell4, six types of World classes are offically supported now: LatticeWorld, EGFRDWorld, BDWorld, MesoscopicWorld, GillespieWorld, and ODEWorld. In this section, the common interfaces of these classes are introduced.
World classes accept different sets of arguments. However, at least, all World classes can be instantiated only with their size, named edge_lengths. The type of edge_lengths is Real3, which represents a triplet of Reals. In E-Cell4, all 3-dimensional positions are treated as a Real3.
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
from ecell4.meso import MesoscopicWorld
from ecell4.egfrd import EGFRDWorld
edge_lengths = Real3(1, 2, 3)
w1 = GillespieWorld(edge_lengths)
w2 = ODEWorld(edge_lengths)
w3 = LatticeWorld(edge_lengths)
w4 = BDWorld(edge_lengths)
w5 = MesoscopicWorld(edge_lengths)
w6 = EGFRDWorld(edge_lengths)
A World has getter methods for the size and volume.
In [2]:
print(tuple(w1.edge_lengths()), w1.volume())
print(tuple(w2.edge_lengths()), w2.volume())
print(tuple(w3.edge_lengths()), w3.volume())
print(tuple(w4.edge_lengths()), w4.volume())
print(tuple(w5.edge_lengths()), w5.volume())
print(tuple(w6.edge_lengths()), w6.volume())
Next, let's add molecules into the World. Here, you must give Species attributed with "radius" and "D" for EGFRDWorld, BDWorld or LatticeWorld to tell the shape of molecules. Positions of the molecules are randomly determined by the World if needed.
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w1.add_molecules(Species("A", "0.0025", "1"), 10)
w2.add_molecules(Species("A", "0.0025", "1"), 10)
w3.add_molecules(Species("A", "0.0025", "1"), 10)
w4.add_molecules(Species("A", "0.0025", "1"), 10)
w5.add_molecules(Species("A", "0.0025", "1"), 10)
w6.add_molecules(Species("A", "0.0025", "1"), 10)
Once binding a NetworkModel to the World, you don't need to give attributes explicitly. The World will ask attributes to the bound NetworkModel.
In [4]:
m = NetworkModel()
m.add_species_attribute(Species("A", "0.0025", "1"))
m.add_species_attribute(Species("B", "0.0025", "1"))
w1.bind_to(m)
w2.bind_to(m)
w3.bind_to(m)
w4.bind_to(m)
w5.bind_to(m)
w6.bind_to(m)
w1.add_molecules(Species("B"), 20)
w2.add_molecules(Species("B"), 20)
w3.add_molecules(Species("B"), 20)
w4.add_molecules(Species("B"), 20)
w5.add_molecules(Species("B"), 20)
w6.add_molecules(Species("B"), 20)
Similarly, remove_molecules and num_molecules are also available.
In [5]:
w1.remove_molecules(Species("B"), 5)
w2.remove_molecules(Species("B"), 5)
w3.remove_molecules(Species("B"), 5)
w4.remove_molecules(Species("B"), 5)
w5.remove_molecules(Species("B"), 5)
w6.remove_molecules(Species("B"), 5)
In [6]:
print(w1.num_molecules(Species("A")), w2.num_molecules(Species("A")), w3.num_molecules(Species("A")), w4.num_molecules(Species("A")), w5.num_molecules(Species("A")), w6.num_molecules(Species("A")))
print(w1.num_molecules(Species("B")), w2.num_molecules(Species("B")), w3.num_molecules(Species("B")), w4.num_molecules(Species("B")), w5.num_molecules(Species("B")), w6.num_molecules(Species("B")))
World class also owns a simulation time.
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print(w1.t(), w2.t(), w3.t(), w4.t(), w5.t(), w6.t())
w1.set_t(1.0)
w2.set_t(1.0)
w3.set_t(1.0)
w4.set_t(1.0)
w5.set_t(1.0)
w6.set_t(1.0)
print(w1.t(), w2.t(), w3.t(), w4.t(), w5.t(), w6.t())
Finally, you can save/load the state of a World into/from a HDF5 file.
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# w1.save("gillespie.h5")
# w2.save("ode.h5")
# w3.save("lattice.h5")
# w4.save("bd.h5")
# w5.save("meso.h5")
# w6.save("egfrd.h5")
del w1, w2, w3, w4, w5, w6
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w1 = GillespieWorld()
w2 = ODEWorld()
w3 = LatticeWorld()
w4 = BDWorld()
w5 = MesoscopicWorld()
w6 = EGFRDWorld()
print(w1.t(), tuple(w1.edge_lengths()), w1.volume(), w1.num_molecules(Species("A")), w1.num_molecules(Species("B")))
print(w2.t(), tuple(w2.edge_lengths()), w2.volume(), w2.num_molecules(Species("A")), w2.num_molecules(Species("B")))
print(w3.t(), tuple(w3.edge_lengths()), w3.volume(), w3.num_molecules(Species("A")), w3.num_molecules(Species("B")))
print(w4.t(), tuple(w4.edge_lengths()), w4.volume(), w4.num_molecules(Species("A")), w4.num_molecules(Species("B")))
print(w5.t(), tuple(w5.edge_lengths()), w5.volume(), w5.num_molecules(Species("A")), w5.num_molecules(Species("B")))
print(w6.t(), tuple(w6.edge_lengths()), w6.volume(), w6.num_molecules(Species("A")), w6.num_molecules(Species("B")))
In [10]:
# w1.load("gillespie.h5")
# w2.load("ode.h5")
# w3.load("lattice.h5")
# w4.load("bd.h5")
# w5.load("meso.h5")
# w6.load("egfrd.h5")
print(w1.t(), tuple(w1.edge_lengths()), w1.volume(), w1.num_molecules(Species("A")), w1.num_molecules(Species("B")))
print(w2.t(), tuple(w2.edge_lengths()), w2.volume(), w2.num_molecules(Species("A")), w2.num_molecules(Species("B")))
print(w3.t(), tuple(w3.edge_lengths()), w3.volume(), w3.num_molecules(Species("A")), w3.num_molecules(Species("B")))
print(w4.t(), tuple(w4.edge_lengths()), w4.volume(), w4.num_molecules(Species("A")), w4.num_molecules(Species("B")))
print(w5.t(), tuple(w5.edge_lengths()), w5.volume(), w5.num_molecules(Species("A")), w5.num_molecules(Species("B")))
print(w6.t(), tuple(w6.edge_lengths()), w6.volume(), w6.num_molecules(Species("A")), w6.num_molecules(Species("B")))
del w1
del w2
del w3
del w4
del w5
del w6
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# print(GillespieWorld("gillespie.h5").t())
# print(ODEWorld("ode.h5").t())
# print(LatticeWorld("lattice.h5").t())
# print(BDWorld("bd.h5").t())
# print(MesoscopicWorld("meso.h5").t())
# print(EGFRDWorld("egfrd.h5").t())
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