# Smoldyn configuration file to test wildcards in reactions
# This file produces a multimeric complex with structure A-B-B-A


define AB_ON	10
define AB_OFF	0.05
define BB_ON	8
define BB_OFF	0.03
define A0	10000
define B0	10000

# Graphical output
graphics opengl_good

# System space and time definitions
dim 3
boundaries x 0 100 p
boundaries y 0 100 p
boundaries z 0 100 p
time_start 0
time_stop 20
time_step 0.05

# Molecular species and their properties
species A B
difc A 2
difc B 1
color A red
color B blue
display_size A 1
display_size B 1

# Reactions
reaction_rule ABon	A + B|BB|BB|ABB -> AB|ABB|ABB|ABBA	AB_ON
reaction_rule ABoff	AB|ABB|ABBA|ABBA -> A + B|BB|ABB|ABB	AB_OFF
reaction_rule BBon1	B + B|AB -> BB|ABB			BB_ON
reaction_rule BBon2	AB + AB -> ABBA				BB_ON
reaction_rule BBoff	*BB* -> *B + *B				BB_OFF

expand_rules all

# initial molecules
mol A0 A u u u
mol B0 B u u u

output_files abbaout.txt
output_format csv
cmd i 0 20 0.5 molcount abbaout.txt

#text_display time A B AB BB ABB ABBA

end_file