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ReactionNetworks :: reactionNetwork

reactionNetwork -- creates a reaction network

Synopsis

Description

Create a reaction network from a string.

i1 : N = reactionNetwork "A <--> 2B, A + C <--> D, B + E --> A + C, D --> B+E"

o1 = A-->2B
     2B-->A
     A+C-->D
     D-->A+C
     D-->B+E
     B+E-->A+C

o1 : ReactionNetwork

Create a reaction network from a list.

i2 : N = reactionNetwork {"S_0+E <--> X_1", "X_1 --> S_1+E",
                          "S_1+E <--> X_2", "X_2 --> S_2+E",
                          "S_1+F <--> Y_1", "Y_1 --> S_0+F",
                          "S_2+F <--> Y_2", "Y_2 --> S_1+F"}

o2 = 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

o2 : ReactionNetwork

Create a reaction network including the empty set.

i3 : N = reactionNetwork ({"A --> 0", "0 --> A"}, NullSymbol => "0")

o3 = A-->0
     0-->A

o3 : ReactionNetwork

The user may view specific information stored in the reaction network, such as species, complexes, etc.

i4 : N = reactionNetwork "A <--> 2B, A + C <--> D, B + E --> A + C, D --> B+E"

o4 = A-->2B
     2B-->A
     A+C-->D
     D-->A+C
     D-->B+E
     B+E-->A+C

o4 : ReactionNetwork
i5 : N.Species

o5 = {A, B, C, D, E}

o5 : List
i6 : N.Complexes

o6 = {| 1 0 0 0 0 |, | 0 2 0 0 0 |, | 1 0 1 0 0 |, | 0 0 0 1 0 |, | 0 1 0 0 1
     ------------------------------------------------------------------------
     |}

o6 : List
i7 : N.ReactionGraph

o7 = Digraph{0 => {1}   }
             1 => {0}
             2 => {3}
             3 => {2, 4}
             4 => {2}

o7 : Digraph

Or the user may view all stored information about a reaction network:

i8 : N = reactionNetwork "A <--> 2B, A + C <--> D, B + E --> A + C, D --> B+E"

o8 = A-->2B
     2B-->A
     A+C-->D
     D-->A+C
     D-->B+E
     B+E-->A+C

o8 : ReactionNetwork
i9 : peek N

o9 = ReactionNetwork{Complexes => {| 1 0 0 0 0 |, | 0 2 0 0 0 |, | 1 0 1 0 0 |, | 0 0 0 1 0 |, | 0 1 0 0 1 |}}
                     ConcentrationRates => null
                     InitialValues => null
                     NullIndex => -1
                     NullSymbol => 
                     ReactionGraph => Digraph{0 => {1}   }
                                              1 => {0}
                                              2 => {3}
                                              3 => {2, 4}
                                              4 => {2}
                     ReactionRates => null
                     ReactionRing => null
                     Species => {A, B, C, D, E}

See also

Ways to use reactionNetwork :