# omniReceptor.txt

##########################################################################
## 
## Simple Scaffold Model
##
## Notes: 
## This model is currently a simple proof-of-concept for how to use 
## libmoleculizer along with Smoldyn to generate some networks.  
## 
##########################################################################

######################
## Preamble
## 

## Some graphics parameters
graphics opengl_good
graphic_delay 100

dim 3
max_species 10000
max_surface 3
max_compartment 3

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

######################
## Surfaces
## 

## This is how you define a boundry that is contained in the rectangle
## with the two corners (0,0,0) and (100,100,100).
## It's front of the boundry faces it's interior. 

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 
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


## This creates a spherical object called the cell with center at
## (50,50,50), a radius of 30, and its front on its inside.

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  
end_surface


######################
## Compartments
## 

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

start_compartment environment
compartment equalnot interior
end_compartment 

######################
## Moleculizer Stuff
##

start_rules
=== Modifications =====================
     name = None, mass = 0.0;
     name = Phosphorylated, mass = 42.0;
     name = DoublyPhosphorylated, mass = 84.0;
     name = GDP, mass = 100.0;
     name = GTP, mass = 110.0;

=== Molecules ===============================
   alpha,
	mass = 100.0;

    # The receptor
    ReceptorGpa1Complex(to-Ste4 { GDP-bound-shape, GTP-bound-shape},  to-alpha, *GXP-site { GDP, GTP} ), 
   	mass = 100.0;

    Ste4(to-Gpa1, to-Ste5 { default, obstructed}, to-Ste20 { default, obstructed} ),
         mass = 100.0;

    Ste20(to-Ste4),
        mass = 100.0;

    Ste5( to-Ste4, to-Ste11, to-Ste7, to-Fus3),
         mass = 100.0;

    Ste11( to-Ste5, *PhosSite { None, Phosphorylated, DoublyPhosphorylated }),
         mass = 100.0;

    Ste7( to-Ste5, *PhosSite { None, Phosphorylated, DoublyPhosphorylated } ),
         mass = 100.0;

    Fus3( to-Ste5, *PhosSite { None, Phosphorylated, DoublyPhosphorylated } ),
         mass = 100.0;

=== Explicit-Species ====================
    ReceptorGpa1Complex(to-Ste4!1).Ste4(to-Gpa1!1), 
        name = ReceptorBoundGpa;

=== Allosteric-Classes =======

    ReceptorGpa1Complex( *GXP-site { GTP }, to-Ste4 { GTP-bound-shape <- * } );
    ReceptorGpa1Complex( *GXP-site { GDP }, to-Ste4 { GDP-bound-shape <- * } );

    Ste4( to-Gpa1!1, to-Ste5 { obstructed <- * }, to-Ste20 { obstructed <- *} ).ReceptorGpa1Complex( to-Ste4!1);

=== Association-Reactions =====
    #
    # alpha/Receptor Binding
    #

    alpha() + ReceptorGpa1Complex(to-alpha) -> alpha(!1).ReceptorGpa1Complex(to-alpha!1),
    	   kon = 10000.0,
	   koff = 1.0;

    ReceptorGpa1Complex( to-Ste4 { GDP-bound-shape } ) + Ste4( to-Gpa1 ) -> ReceptorGpa1Complex( to-Ste4!1 ).Ste4( to-Gpa1!1 ),
           kon = 100.0,
           koff = 1.0,
         ReceptorGpa1Complex( to-Ste4 { GTP-bound-shape } ) + Ste4( to-Gpa1 ) -> ReceptorGpa1Complex( to-Ste4!1 ).Ste4( to-Gpa1!1 ),
             kon = 1.0,
             koff = 100.0;

    Ste4( to-Ste5) + Ste5( to-Ste4) -> Ste4( to-Ste5!1).Ste5( to-Ste4!1),
            kon = 100.0,
            koff = 1.0,
        Ste4( to-Ste5 { obstructed} ) + Ste5( to-Ste4) -> Ste4( to-Ste5!1).Ste5( to-Ste4!1),
             kon = 1.0,
             koff = 100.0;

    Ste4(to-Ste20) + Ste20( to-Ste4) -> Ste4( to-Ste20!1).Ste20( to-Ste4!1),
             kon = 100.0,
             koff = 1.0,
       Ste4(to-Ste20 {obstructed} ) + Ste20( to-Ste4) -> Ste4( to-Ste20!1).Ste20( to-Ste4!1),
              kon = 1.0,
	      koff = 100.0;

    Ste5(to-Ste11) + Ste11(to-Ste5) -> Ste5(to-Ste11!1).Ste11(to-Ste5!1),
             kon = 100.0,
             koff = 1.0;

    Ste5(to-Ste7) + Ste7(to-Ste5) -> Ste5(to-Ste7!1).Ste7(to-Ste5!1),
             kon = 100.0,
             koff = 1.0;

    Ste5(to-Fus3) + Fus3(to-Ste5) -> Ste5(to-Fus3!1).Fus3(to-Ste5!1),
             kon = 100.0,
             koff = 1.0;

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

    alpha(!1).ReceptorGpa1Complex(to-alpha!1, *GXP-site { GDP} ) -> alpha(!1).ReceptorGpa1Complex(to-alpha!1, *GXP-site { GTP} ),
          k = 10000.0;
          
    ReceptorGpa1Complex(*GXP-site { GTP } ) -> ReceptorGpa1Complex( *GXP-site { GDP } ),
          k = 10.0;

    # The two Ste20->Ste11 Functions
    Ste5(to-Ste4!1,to-Ste11!3).Ste4(to-Ste5!1,to-Ste20!2).Ste20(to-Ste4!2).Ste11(to-Ste5!3, *PhosSite {None} ) -> Ste5(to-Ste4!1,to-Ste11!3).Ste4(to-Ste5!1,to-Ste20!2).Ste20(to-Ste4!2).Ste11(to-Ste5!3, *PhosSite {Phosphorylated} ),
         k = 100.0;

    Ste5(to-Ste4!1,to-Ste11!3).Ste4(to-Ste5!1,to-Ste20!2).Ste20(to-Ste4!2).Ste11(to-Ste5!3, *PhosSite {Phosphorylated} ) -> Ste5(to-Ste4!1,to-Ste11!3).Ste4(to-Ste5!1,to-Ste20!2).Ste20(to-Ste4!2).Ste11(to-Ste5!3, *PhosSite {DoublyPhosphorylated} ),
         k = 100.0;

    #####
    # The four Ste11 -> Ste7 transfer functions.
    #
    Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {None} ).Ste11(to-Ste5!1, *PhosSite {Phosphorylated} )-> Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Ste11(to-Ste5!1, *PhosSite {None} ),
          k = 100.0;

    Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Ste11(to-Ste5!1, *PhosSite {Phosphorylated} )-> Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {DoublyPhosphorylated} ).Ste11(to-Ste5!1, *PhosSite {None} ),
          k = 100.0;

    Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Ste11(to-Ste5!1, *PhosSite {DoublyPhosphorylated} )-> Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {DoublyPhosphorylated} ).Ste11(to-Ste5!1, *PhosSite {Phosphorylated} ),
          k = 100.0;

    Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {None} ).Ste11(to-Ste5!1, *PhosSite {DoublyPhosphorylated} )-> Ste5(to-Ste11!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Ste11(to-Ste5!1, *PhosSite {Phosphorylated} ),
          k = 100.0;
    #####
    # The four Ste7 -> Fus3 transfer function
    #
    Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Fus3(to-Ste5!1, *PhosSite {None} )-> Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {None} ).Fus3(to-Ste5!1, *PhosSite {Phosphorylated} ),
          k = 100.0;

    Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Fus3(to-Ste5!1, *PhosSite {Phosphorylated} )-> Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {None} ).Fus3(to-Ste5!1, *PhosSite {DoublyPhosphorylated} ),
          k = 100.0;

    Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {DoublyPhosphorylated} ).Fus3(to-Ste5!1, *PhosSite {None} )-> Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Fus3(to-Ste5!1, *PhosSite {Phosphorylated} ),
          k = 100.0;

    Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {DoublyPhosphorylated} ).Fus3(to-Ste5!1, *PhosSite {Phosphorylated} )-> Ste5(to-Fus3!1, to-Ste7!2).Ste7(to-Ste5!2, *PhosSite {Phosphorylated} ).Fus3(to-Ste5!1, *PhosSite {DoublyPhosphorylated} ),
          k = 100.0;


=== Species-Classes =====================
    ReceptorGpa1Complex(to-alpha!1).alpha(!1),
	name = BoundAlpha;

    ReceptorGpa1Complex(to-alpha!1, to-Ste4!2).alpha(!1).Ste4(to-Gpa1!2),
        name = BoundUnit;

    Fus3(to-Ste5, *PhosSite {DoublyPhosphorylated}),
        name = DoublyPhosphorylatedFus3;
   
end_rules


##################
## Defining species
##

max_mol 40000
species alpha ReceptorGpa1Complex Ste4 Ste5

difc alpha 100
difc ReceptorGpa1Complex 20
difc Ste4 10
difc Ste5 20

display_size alpha 0.2
display_size ReceptorGpa1Complex .5
display_size Ste4 .3
display_size Ste5 .6

color alpha 0 1 0 


species_class_color BoundAlpha(all) 0 0 1
species_class_display_size BoundAlpha(all) 5.0

species_class_color BoundUnit(all) 1 0 0
species_class_display_size BoundUnit(all) 5.0

######################
## Create species
##

mol 7000 alpha 15 15 15
surface_mol 100 ReceptorGpa1Complex(back) cell all all
compartment_mol 200 Ste5 interior

time_start 0
time_stop 5
time_step 0.01

output_files stdout

cmd b molcountheader stdout
cmd a molcountheader stdout
cmd b molcount stdout
cmd a molcount stdout
cmd b pause

end_file