# receptor-on-surface.txt
#  This model extends the moleculizer-smallmol-example2.txt model, by
#  adding a surface, placing receptor on the outside of that surface,
#  and having receptor/ligand interactions done in that way.  

graphics opengl_good
graphic_delay 100

dim 3

boundaries 0 0 100 r
boundaries 1 0 100 r
boundaries 2 0 100 r

max_species 100
max_surface 3
max_compartment 3

start_surface boundary
action both all reflect
color both 1 1 1
polygon both edge 
max_panels rect 6
panel rect +0 0 0 0 100 100 # This is a panel perpindicular to the x
                              # axis (0) -- in the yz plane with one
                              # corner at (0,0,0), extends for 100 in
                              # the y dir and 100 in the z dir.
panel rect -0 100 0 0 100 100 
panel rect -1 0 100 0 100 100 
panel rect +1 0 0 0 100 100
panel rect -2 0 0 100 100 100 
panel rect +2 0 0 0 100 100
end_surface


start_surface cell
action both all reflect
color both 1 1 1
polygon both edge
max_panels sph 1
panel sph 50 50 50 -30 20 20  # This should draw as sphere with center
                              # (50, 50, 50), radius 30, the front on
                              # the inside of the sphere, and with 20
                              # longitudinal samplings, 20 latitudinal
                              # samplings in order to define the
                              # triangulation of the surface.
end_surface


# Define a compartment, the cytosol of the cell 
start_compartment interior
surface cell
point 50 50 50                   
end_compartment 

start_compartment exterior
compartment equalnot interior
end_compartment 


start_rules

===== Molecules ======================
      Receptor(ligand_site), mass = 10000.0;
      Ligand, mass = 100.0;

===== Association-Reactions =========	

      Receptor(ligand_site) + Ligand -> Receptor(ligand_site!1).Ligand(!1),
      	      kon = 100,
	      koff = 10;

===== Explicit-Species ===============

      Receptor(ligand_site!1).Ligand(!1),
	name = BoundReceptor;

end_rules

species Receptor Ligand BoundReceptor

difc Receptor 10.0
difc Ligand 100.0

max_mol 10000;

color Receptor(all) 0 1 0
color Ligand(all) 1 0 0
color BoundReceptor(all) 0 0 1

display_size Receptor 1.0
display_size Ligand .7
display_size BoundReceptor 2.0

time_start 0
time_stop 100
time_step 0.01

boundaries 0 0 100 r
boundaries 1 0 100 r
boundaries 2 0 100 r


surface_mol 100 Receptor(back) cell all all
mol 100 Ligand 10 10 10

cmd b pause

end_file


color