gillespie.rb in y_petri-2.1.31

- old
+ new
@@ -1,25 +1,26 @@
 #! /usr/bin/ruby
-# coding: utf-8
-
-# ==============================================================================
-# 
 # encoding: utf-8
 
 require 'y_petri'
-require 'sy'       # This pathway model uses 'sy' metrology domain model.
-require 'mathn'    # Standard library 'mathn' is required.
-include YPetri     # pull in the DSL
+require 'sy'
+require 'mathn'
+include YPetri
 
 A = Place m!: 10
 B = Place m!: 10
-A2B = Transition s: { A: -1, B: 1 }, rate: 0.1
-B2A = Transition s: { A: 1, B: -1 }, rate: 0.05
+AB = Place m!: 0
+AB_association = Transition s: { A: -1, B: -1, AB: 1 }, rate: 0.1
+AB_dissociation = Transition s: { AB: -1, A: 1, B: 1 }, rate: 0.1
+A2B = Transition s: { A: -1, B: 1 }, rate: 0.05
+B2A = Transition s: { A: 1, B: -1 }, rate: 0.07
 
-set_step 1 # in seconds
-set_target_time 100
+set_step 1
+set_target_time 50
 set_sampling 1
 set_simulation_method :gillespie
-sim = new_simulation guarded: false
+
 run!
+
+print_recording
 
 plot_state