#!/usr/bin/env python
# coding: utf-8

# # MinDE System with Mesoscopic Simulator

# Fange D, Elf J (2006) Noise-Induced Min Phenotypes in E. coli. PLoS Comput Biol 2(6): e80. doi:10.1371/journal.pcbi.0020080

# In[1]:


get_ipython().run_line_magic('matplotlib', 'inline')
from ecell4 import *
from ecell4_base.core import *
from ecell4_base import meso


# Declaring `Species` and `ReactionRule`s:

# In[2]:


with species_attributes():
    D | DE | {"D": 0.01, "location": "M"}
    D_ADP | D_ATP | E | {"D": 2.5, "location": "C"}

with reaction_rules():
    D_ATP + M > D | 0.0125
    D_ATP + D > D + D | 9e+6 * (1e+15 / N_A)
    D + E > DE | 5.58e+7 * (1e+15 / N_A)
    DE > D_ADP + E | 0.7
    D_ADP > D_ATP | 0.5

m = get_model()


# Make a `World`. The second argument, `0.05`, means its subvolume length:

# In[3]:


w = meso.World(Real3(4.6, 1.1, 1.1), 0.05)
w.bind_to(m)


# Make a structures. `Species` `C` is for cytoplasm, and `M` is for membrane:

# In[4]:


rod = Rod(3.5, 0.55, w.edge_lengths() * 0.5)
w.add_structure(Species("C"), rod)
w.add_structure(Species("M"), rod.surface())


# Throw-in molecules:

# In[5]:


w.add_molecules(Species("D_ATP"), 2001)
w.add_molecules(Species("D_ADP"), 2001)
w.add_molecules(Species("E"), 1040)


# Run a simulation for 120 seconds. Two `Observer`s below are for logging. `obs1` logs only the number of molecules, and `obs2` does a whole state of the `World`.

# In[6]:


sim = meso.Simulator(w)
obs1 = FixedIntervalNumberObserver(0.1, [sp.serial() for sp in m.list_species()])
obs2 = FixedIntervalHDF5Observer(1.0, 'minde%03d.h5')


# In[7]:


duration = 120
sim.run(duration, (obs1, obs2))


# Visualize the final state of the `World`:

# In[8]:


plotting.plot_world(w, species_list=('D', 'DE'))


# Plot a time course of the number of molecules:

# In[9]:


show(obs1)


# In[10]:


plotting.plot_movie(obs2, species_list=('D', 'DE'))


# In[ ]: