"""
Description:
Box of A & B with reactions:
- A -> 0 decay
- A -> B decay
- A + B -> C irreversible
- A + B <-> C reversible
"""
import pymcell as pm
# Make worlds:
world = pm.make_world()
# Add objects:
box = pm.make_object(name='Box', type='CUBE') # default size and position
world.add_object(box)
# Add species:
mol_a = pm.make_species(name='a') # red, Sphere_1, 1e-6, and VOLUME by default
mol_b = pm.make_species(name='b', color=[0, 0, 1]) # blue
mol_c = pm.make_species(name='c', color=[0, 1, 0]) # green
world.add_species(mol_a, mol_b, mol_c)
# Add release patterns:
rel_a_b = pm.make_release_pattern(species_list=[mol_a, mol_b],
release_region=box)
world.add_release_pattern(rel_a_b)
# Add reactions:
""" Description: Surface classes - Box with one transparent side to molecule A - Box with absorptive side to molecule A - Box with concentration clamp of A on one side and absorptive on the opposing side """ import pymcell as pm # Make worlds: world_trans = pm.make_world() # "name = " defaults to "World_1" world_abs = pm.make_world() # "name = " defaults to "World_2" world_clamp_abs = pm.make_world() # Add objects: box = pm.make_object(name='Box', type='CUBE') # default size and position world_trans.add_object(box) world_abs.add_object(box) world_clamp_abs.add_object(box) # Add species: mol_a = pm.make_species(name='a') # red, Sphere_1, 1e-6, and VOLUME by default world_trans.add_species(mol_a) world_abs.add_species(mol_a) world_clamp_abs.add_species(mol_a) # Add surface classes: trans_surf = pm.make_surface_class(type='TRANSPARENT', molecules=[mol_a]) abs_surf = pm.make_surface_class(type='ABSORPTIVE', molecules=[mol_a])