# transformation-reactions.txt # This model illustrates how to make a basic small-mol/molecule # interaction, in this case between Receptor and Ligand. graphics opengl_good graphic_delay 100 dim 3 max_species 100 start_rules ===== Modifications ================== name = None, mass = 0.0; name = Phosphorylated, mass = 42.0; ===== Molecules ====================== ATP, mass = 100.0; ADP, mass = 100.0; Firefly(axp_site, *PhosSite{ None, Phosphorylated} ), mass = 10000.0; ===== Association-Reactions ========= Firefly( axp_site) + ATP -> Firefly(axp_site!1).ATP(!1), kon = 500.0, koff = 0.0; Firefly( axp_site) + ADP -> Firefly(axp_site!1).ADP(!1), kon = 0.0, koff = 500.0; ===== Transformation-Reactions ========= Firefly( axp_site!1, *PhosSite{ None} ).ATP(!1) -> Firefly( axp_site!1, *PhosSite{ Phosphorylated} ).ADP(!1), k = 100.0; Firefly( *PhosSite{Phosphorylated} ) -> Firefly( *PhosSite{Phosphorylated} ), k = 100.0; ===== Species-Classes ================ Firefly(*PhosSite{ Phosphorylated} ), name = On; Firefly(*PhosSite{ None} ), name = Off; end_rules species ATP ADP Firefly difc Firefly 20 difc ATP 40.0 difc ADP 40.0 max_mol 10000; color Firefly 0 1 1 display_size ATP .4 display_size ADP .4 species_class_display_size Off 1.0 species_class_display_size On 1.6 species_class_color Off 0 0 1 species_class_color On 1 1 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 mol 1 Firefly 50 50 50 mol 10 ATP 50 50 50 cmd b pause end_file