# cmdtrial.txt
# This model uses basic-oligo-rules.mzr, which was created from
# basicOligoRules.txt with moleculizer's new language.

# graphics opengl

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

==== Modifications ===========
==== Molecules     ===========
A(left{default, occluded}, right{default, occluded}),
        mass = 1000.0;

==== Explicit-Allostery  ======


==== Allosteric-Classes ======
A(left{occluded <-* }, right!1).A(left!1, right!2 ).A(left!2, right!3).A(left!3, right!4).A(left!4, right {occluded <- *});

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

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

A(left) + A(right) -> A(left!1).A(right!1),
        kon = 1000,
        koff = 1;

#         A(left {occluded} ) + A(right {occluded} ) -> A(left!1).A(right!1),
#         kon = 0,
#         koff = 10000;

    
=== Species-Classes ======

A(left!1).A(right!1), name=lengthtwo;
A(right!1).A(left!1,right!2).A(left!2,right!3).A(left!3)
	, name=lengthfour;

A(right!1).A(left!1,right!2).A(left!2,right!3).A(left!3,right!4).A(left!4,right!5).A(left!5), name=lengthsix;

end_rules


max_network_species 11

species A
max_mol 1500

difc A          999


color A      1 0 0
display_size A 1.0

species_class_display_size lengthtwo 2.0
species_class_display_size lengthfour 4.0
species_class_display_size lengthsix 14.0

species_class_color lengthfour 1 0 0 
species_class_color lengthsix 0 0 1 


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 pause

cmd b speciesstreamheader stdout
cmd b speciesstreamcount stdout