substitute(ReactionNetwork,List) -- substitute species names in reaction network

Synopsis

Function: substitute

Description

The user may choose to change the symbols for one or more of the species participating in the reaction. This can be done in the following manner. To rename one of the species:

i1 : N = twoSiteModificationG()

o1 = S_0+E-->X_1
     X_1-->S_0+E
     X_1-->E+S_1
     E+S_1-->X_2
     X_2-->E+S_1
     X_2-->E+S_2
     S_1+F-->Y_1
     Y_1-->S_1+F
     Y_1-->S_0+F
     S_2+F-->Y_2
     Y_2-->S_1+F
     Y_2-->S_2+F

o1 : ReactionNetwork

i2 : sub(N, {"S_0" => "A"})

o2 = A+E-->X_1
     X_1-->A+E
     X_1-->E+S_1
     E+S_1-->X_2
     X_2-->E+S_1
     X_2-->E+S_2
     S_1+F-->Y_1
     Y_1-->S_1+F
     Y_1-->A+F
     S_2+F-->Y_2
     Y_2-->S_1+F
     Y_2-->S_2+F

o2 : ReactionNetwork

Similarly, more species labels may be replaced.

i3 : sub(N, {"S_0" => "A", "X_1" => "B", "X_2" => "C", "S_1" => "D"})

o3 = A+E-->B
     B-->A+E
     B-->E+D
     E+D-->C
     C-->E+D
     C-->E+S_2
     D+F-->Y_1
     Y_1-->D+F
     Y_1-->A+F
     S_2+F-->Y_2
     Y_2-->D+F
     Y_2-->S_2+F

o3 : ReactionNetwork

Ways to use this method: