removed vs code stuff

Project.toml

@@ -4,6 +4,7 @@ authors = ["st elmo <stelmozors@gmail.com>"]
 version = "0.1.0"
 
 [deps]
+Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 GLPK = "60bf3e95-4087-53dc-ae20-288a0d20c6a6"
 GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
 Gurobi = "2e9cd046-0924-5485-92f1-d5272153d98b"
@@ -15,8 +16,10 @@ JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MATLAB = "10e44e05-a98a-55b3-a45b-ba969058deb6"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
+PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Tulip = "6dd1b50a-3aae-11e9-10b5-ef983d2400fa"
 

src/CobraTools.jl

@@ -18,6 +18,7 @@ using Ipopt
 # Gibbs
 using Measurements
 using Statistics
+using PyCall
 
 include("global_cobratools.jl")
 

src/cobratools-workspace.code-workspace

-{
-	"folders": [
-		{
-			"path": ".."
-		}
-	],
-	"settings": {
-	}
-}
\ No newline at end of file

src/gibbs_tools.jl

@@ -19,42 +19,5 @@ function Base.show(io::IO, gibbs::Gibbs)
 end
 
 function mapGibbs(rxns::Array{Reaction, 1}; ph="7.0", T=298.15, R=8314.46261815324)
-    gibbs_data = JLD.load(joinpath("data", "gibbs_$ph.jld"), "gibbs")
-    name_mapping = JLD.load(joinpath("data", "bigg_to_kegg.jld"), "bigg_to_kegg") # need to fix for other name spaces
-    ΔG⁰s = Gibbs[]
-    ΔGs = Gibbs[]
-    for i in eachindex(rxns)
-        id = rxns[i].id
-        if haskey(name_mapping, id)
-            gs = Measurement{Float64}[]
-            for kegg in name_mapping[id]
-                if haskey(gibbs_data, kegg)
-                    push!(gs, gibbs_data[kegg][1] ± gibbs_data[kegg][2])
-               end
-            end
-            if isempty(gs)
-                println(id)
-                push!(ΔG⁰s, Gibbs(0.0 ± 0.0)) # missing 
-                push!(ΔGs, Gibbs(0.0 ± 0.0)) # missing    
-            else
-                mg = mean(gs)
-                Q = 1.0
-                for (met, stoich) in rxns[1].metabolites
-                    if stoich > 0
-                        Q = Q * (met.concentration^stoich)
-                    else
-                        Q = Q / (met.concentration^stoich)
-                    end
-                end
-                gadj = mg + R * T * log(Q)
-                push!(ΔG⁰s, Gibbs(mg)) # missing 
-                push!(ΔGs, Gibbs(gadj)) # missing    
-            end
-        else
-            println(id)
-            push!(ΔG⁰s, Gibbs(0.0 ± 0.0)) # missing 
-            push!(ΔGs, Gibbs(0.0 ± 0.0)) # missing
-        end
-    end
-    return ReactionGibbs(rxns, ΔG⁰s, ΔGs)
+    
 end
\ No newline at end of file