# allreceptor.txt

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 ===========
      Ligand, mass = 100.0;
      Receptor(ligand_site, secondary_site {Occluded, Active}), mass = 10000.0;
      SecondMessenger( receptor-site, target-site {Inactive, Active}, *PhosSite{none, Phosphorylated}), mass = 10000.0;
      Target( PrimarySite ), mass = 10000;

==== Allosteric-Classes  ======
     SecondMessenger( target-site { Active <- *}, *PhosSite {Phosphorylated} );
     Receptor( ligand_site!1, secondary_site {Active <-*} ).Ligand(!1);

==== Allosteric-Species =======

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

     SecondMessenger(binding-site!1).Target(PrimarySite!1),
	name = TargetComplex;

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

      Receptor(secondary_site) + SecondMessenger( site ) <-> Receptor(secondary_site!1).SecondMessenger( site!1 ),
             kon = 0.0,
	     koff = 10000,

	     Receptor(secondary_site {Active} ) + SecondMessenger( site ) <-> Receptor(secondary_site!1).SecondMessenger( site!1 ),
	         kon = 100.0,
		 koff = 0.0;

       SecondMessenger(target-site) + Target( primary-site ) <-> SecondMessenger(target-site).Target( primary-site ),
                 kon = 0.0,
		 koff = 10000.0,
	     SecondMessenger(target-site {Active}) + Target( primary-site ) <-> SecondMessenger(target-site).Target( primary-site ),
	         kon = 300.0,
		 koff = 0.0;

=== Transformation-Reactions ======

    Receptor( secondary_site!1).SecondMessenger( binding-site!1, *PhosSite {None} ) ->
          Receptor( secondary_site!1).SecondMessenger( binding-site!1, *PhosSite {Phosphorylated} ),
	  	k = 100.0;
     
=== Species-Classes ======

end_rules

max_network_species 11

species A
max_mol 1500

difc           999
color A      1 0 0
display_size  1.0





time_start 0
time_stop 10
time_step 0.01

compartment_mol 100 A interior

output_files stdout
cmd b molcountheader stdout
cmd a molcountheader stdout

cmd b molcount stdout
cmd a molcount stdout

cmd b speciesstreamheader stdout
cmd b speciesstreamcount stdout

cmd a speciesstreamheader stdout
cmd a speciesstreamcount stdout

cmd b pause