from neuron import h, rxd
h.load_file('stdrun.hoc')

class Cell:
    def __init__(self):
        self.soma = h.Section()

cell_1 = Cell()
cell_2 = Cell()
ecs = rxd.Extracellular(-55, -55, -55, 55, 55, 55, dx=10, volume_fraction=0.2, tortuosity=1.6)

soma_cell_1 = rxd.Region([cell_1.soma], nrn_region='i', geometry=rxd.Shell(0.8, 1))
soma_cell_2 = rxd.Region([cell_2.soma], nrn_region='i', geometry=rxd.Shell(0.8, 1))
species_x = rxd.Species([ecs,soma_cell_1, soma_cell_2], name='species_x', d=1, charge=1, initial=1,  ecs_boundary_conditions=0)
Species_y = rxd.Species([soma_cell_1, ecs], name='species_y', d=1, charge=1, initial=1,  ecs_boundary_conditions=0)
Species_z = rxd.Species([soma_cell_1], name='species_z', d=1, charge=1, initial=1,  ecs_boundary_conditions=0)
reaction_1 = rxd.Reaction(Species_y >Species_z + species_x, 0.058, regions = [soma_cell_1])

h.finitialize()
h.continuerun(10)
