Update api.jl

adding some more tests to see whether Z*B == netstoichmat(rn)'

test/api.jl

@@ -234,4 +234,193 @@ B = [-1 1 0 0 0 0;
 @test all(Z .== complex_stoich_matrix(rns[6]))
 @test all(B .== complex_incidence_matrix(rns[6]))
 @test all(Δ .== complex_outgoing_matrix(rns[6]))
+
+
+reaction_networks_standard = Vector{ReactionSystem}(undef,10)
+reaction_networks_hill = Vector{ReactionSystem}(undef,10)
+reaction_networks_real = Vector{ReactionSystem}(undef,3)
+### some more networks to test whether Z*B == netstoichmat(rn)' or not. ###
+reaction_networks_standard[1] = @reaction_network begin
+    (p1,p2,p3), ∅ → (X1,X2,X3)
+    (k1,k2), X2 ⟷ X1 + 2X3
+    (k3,k4), X1 ⟷ X3
+    (d1,d2,d3), (X1,X2,X3) → ∅
+end p1 p2 p3 k1 k2 k3 k4 d1 d2 d3
+
+reaction_networks_standard[2] = @reaction_network begin
+    mmr(X2,v1,K1), ∅ → X1
+    mm(X1,v2,K2), ∅ → X2
+    d, X1+X2 → ∅
+end v1 K1 v2 K2 d
+
+reaction_networks_standard[3] = @reaction_network begin
+    mm(X2,v1,K1), ∅ → X1
+    mm(X3,v2,K2), ∅ → X2
+    (k1,k2), X1 ⟷ X3
+    (k3,k4), X3 + X2 ⟷ X4 + X1
+    d, (X1,X2,X3,X4) → ∅
+end v1 K1 v2 K2 k1 k2 k3 k4 d
+
+reaction_networks_standard[4] = @reaction_network begin
+    mmr(X4,v1,K1), ∅ → X1
+    mmr(X1,v2,K2), ∅ → X2
+    mmr(X2,v3,K3), ∅ → X3
+    mmr(X3,v4,K4), ∅ → X4
+    (d1,d2,d3,d4), (X1,X2,X3,X4) → ∅
+end v1 K1 v2 K2 v3 K3 v4 K4 d1 d2 d3 d4
+
+reaction_networks_standard[5] = @reaction_network begin
+    p, ∅ → X1
+    (k1,k2), X1 ⟷ X2
+    (k3,k4), X2 ⟷ X3
+    (k5,k6), X3 ⟷ X4
+    d, X4 → ∅
+end p k1 k2 k3 k4 k5 k6 d
+
+reaction_networks_standard[6] = @reaction_network begin
+    (p1,p2), ∅ → (X1,X2)
+    (k1,k2), 2X1 ⟷ X3
+    (k3,k4), X2 + X3 ⟷ 4X4
+    (k5,k6), X4 + X1 ⟷ 2X3
+    d, (X1,X2,X3,X4) → ∅
+end p1 p2 k1 k2 k3 k4 k5 k6 d
+
+reaction_networks_standard[7] = @reaction_network begin
+    (p1,p2,p3), ∅ → (X1,X2,X3)
+    (k1,k2), X1 + 2X2 ⟷ X4
+    (mm(X3,v1,K1),k3), X4 ⟷ X5
+    (d1,d2,d3,d4,d5), (X1,X2,X3,X4,X5) → ∅
+end p1 p2 p3 k1 k2 k3 v1 K1 d1 d2 d3 d4 d5
+
+reaction_networks_standard[8] = @reaction_network begin
+    p, ∅ → 2X1
+    k1, X1 → X2
+    (k2, k3), X2 → X3
+    d, X3 → ∅
+end p k1 k2 k3 d
+
+reaction_networks_standard[9] = @reaction_network begin
+    (p1,p2,p3), ∅ ⟶ (X1,X2,X3)
+    (d1,d2,d3), (X1,X2,X3) ⟶ ∅
+    (k1,k2), X1 + X2 ⟷ X3
+    (k3,k4), X3 ⟷ X4
+    (k5,k6), X4 ⟷ X1 + X2
+end p1 p2 p3 d1 d2 d3 k1 k2 k3 k4 k5 k6
+
+reaction_networks_standard[10] = @reaction_network begin
+    p, ∅ ⟶ X1
+    (k1,k2), X1 → X2
+    (k3,k4), X2 → X3
+    (k5,k6), X3 → X4
+    (k7,k8), X4 → X5
+    d, X5  ⟶ ∅
+end p k1 k2 k3 k4 k5 k6 k7 k8 d
+
+
+### Network with hill functions ###.
+
+reaction_networks_hill[1] = @reaction_network begin
+    hillr(X2,v1,K1,n1),   ∅ → X1
+    hillr(X1,v2,K2,n2),   ∅ → X2
+    (d1,d2),          (X1,X2) → ∅
+end v1 v2 K1 K2 n1 n2 d1 d2
+
+reaction_networks_hill[2] = @reaction_network begin
+    hillr(X3,v1,K1,n1),   ∅ → X1
+    hillr(X1,v2,K2,n2),   ∅ → X2
+    hillr(X2,v3,K3,n3),   ∅ → X3
+    (d1,d2,d3),          (X1,X2,X3) → ∅
+end v1 v2 v3 K1 K2 K3 n1 n2 n3 d1 d2 d3
+
+reaction_networks_hill[3] = @reaction_network begin
+    hillr(X2,v1,K1,n1), ∅ → X1
+    hill(X1,v2,K2,n2), ∅ → X2
+    d, X1+X2 → ∅
+end v1 K1 n1 v2 K2 n2 d
+
+reaction_networks_hill[4] = @reaction_network begin
+    hillr(X2,v1,K1,n1)*hillr(X3,v1,K1,n1), ∅ → X1
+    hillr(X1,v2,K2,n2)*hillr(X3,v2,K2,n2), ∅ → X2
+    hillr(X1,v3,K3,n3)*hillr(X2,v3,K3,n3), ∅ → X3
+    (d1,d2,d3), (X1,X2,X3)  ⟶ ∅
+end v1 K1 n1 v2 K2 n2 v3 K3 n3 d1 d2 d3
+
+reaction_networks_hill[5] = @reaction_network begin
+    hillr(X2,v1,K1,n1)*hill(X4,v1,K1,n1), ∅ → X1
+    hill(X5,v2,K2,n2), ∅ → X2
+    hill(X3,v3,K3,n3), ∅ → X3
+    hillr(X1,v4,K4,n4), ∅ → X4
+    hill(X2,v5,K5,n5), ∅ → X5
+    (k1,k2), X2 ⟷ X1 + 2X4
+    (k3,k4), X4 ⟷ X3
+    (k5,k6), 3X5 + X1 ⟷ X2
+    (d1,d2,d3,d4,d5), (X1,X2,X3,X4,X5)  ⟶ ∅
+end v1 K1 n1 v2 K2 n2 v3 K3 n3 v4 K4 n4 v5 K5 n5 k1 k2 k3 k4 k5 k6 d1 d2 d3 d4 d5
+
+reaction_networks_hill[6] = @reaction_network begin
+    v/10+hill(X1,v,K,n), ∅ → X1
+    d, X1 → ∅
+end v K n d
+
+reaction_networks_hill[7] = @reaction_network begin
+    v/10 + hill(X1,v,K,n), ∅ → X1 + X2
+    (k1,k2), X1 + X2 ↔ X3
+    k3, X3 → X1
+    d, (X1,X2,X3) → ∅
+end v K n k1 k2 k3 d
+
+reaction_networks_hill[8] = @reaction_network begin
+    hill(X2,v1,K1,n1), ∅ → X1
+    hillr(X1,v2,K2,n2)*hill(X3,v3,K3,n3), ∅ → X2
+    hill(X2,v4,K4,n4), ∅ → X3
+    (d1,d2,d3), (X1,X2,X3) → ∅
+end v1 K1 n1 v2 K2 n2 v3 K3 n3 v4 K4 n4 d1 d2 d3
+
+reaction_networks_hill[9] = @reaction_network begin
+    hill(X1,v1,K1,n1)*hillr(X1,v2,K2,n2), ∅ → X1
+    d, X1 → ∅
+end v1 K1 n1 v2 K2 n2 d
+
+reaction_networks_hill[10] = @reaction_network begin
+    hill(X2,v1,K1,n1), ∅ → X1
+    hillr(X4,v2,K2,n2), ∅ → X2
+    (k1,k2), 2X1 + X2 ⟷ X3
+    (k3,k4), 2X2 + X3 ⟷ X4
+    (k5,k6), X1 + X2 + X3 + X4 ⟷ X5 + X6
+    (d1,d2), (X5,X6) → ∅
+end v1 K1 n1 v2 K2 n2 k1 k2 k3 k4 k5 k6 d1 d2
+
+
+reaction_networks_real[1] = @reaction_network begin
+    v0 + hill(σ,v,K,n), ∅ → (σ+A)
+    deg, (σ,A,Aσ) → ∅
+    (kB,kD), A + σ ↔ Aσ
+    S*kC, Aσ → σ
+end v0 v K n kD kB kC deg S;
+
+# A cell cycle model
+reaction_networks_real[2] = @reaction_network begin
+  k1, 0 --> Y
+  k2p, Y --> 0
+  k2pp*P, Y --> 0
+  (k3p+k3pp*A)/(J3+Po), Po-->P
+  (k4*m)/(J4+P), Y + P --> Y + Po
+end k1 k2p k2pp k3p k3pp A J3 k4 m J4
+#@add_constraint cc_network P+Po=1
+#reaction_networks_real[3] = cc_network
+
+# A bistable switch
+reaction_networks_real[3] = @reaction_network begin
+    d,    (X,Y) → ∅
+    hillr(Y,v1,K1,n1), ∅ → X
+    hillr(X,v2,K2,n2), ∅ → Y
+end d v1 K1 n1 v2 K2 n2
+
+myrn = [reaction_networks_standard;reaction_networks_hill;reaction_networks_real]
+for i in 1:length(myrn)
+    Z = complex_stoich_matrix(myrn[i])
+    B = complex_incidence_matrix(myrn[i])
+    @test all(Z*B .== netstoichmat(myrn[i])')
+end
+