Merge pull request #9 from isaacsas/rssa-fix

rssa str fix

Author: isaacsas

README.md

@@ -20,13 +20,12 @@ fname = "PATH/TO/Repressilator.net"
 prnbng = loadrxnetwork(BNGNetwork(), "BNGRepressilator", fname)
 ```
 Here `BNGNetwork` is a type specifying the file format that is being loaded, and `BNGRepressilator` specifies the type of the generated `min_reaction_network`, see [DiffEqBiological](https://github.com/JuliaDiffEq/DiffEqBiological.jl/). `prnbng` is a `ParsedReactionNetwork` structure with the following fields:
-- `rn`, a DiffEqBiological `min_reaction_network`
+- `rn`, a DiffEqBiological `reaction_network`
 - `u₀`, the initial condition (as a `Vector{Float64}`)
 - `p`, the parameter vector (as a `Vector{Float64}`)
 - `paramexprs`, the parameter vector as a mix of `Numbers`, `Symbols` and `Exprs`. `p` is generated by evaluation of these expressions and symbols.
 - `symstonames`, a `Dict` mapping from the internal `Symbol` of a species used in the generated `min_reaction_network` to a `Symbol` generated from the name in the .net file. This is necessary as BioNetGen can generate exceptionally long species names, involving characters that lead to malformed species names when used with `DiffEqBiological`.
 - `groupstoids`, a `Dict` mapping the `Symbols` (i.e. names) for any species groups defined in the .net file to a vector of indices into `u₀` where the corresponding species are stored.
-- `rnstr`, a string representation of the full DiffEqBiological DSL command that was evaluated to generate the network.
 
 Given `prnbng`, we can construct and solve the corresponding ODE model for the reaction system by
 ```julia
@@ -46,4 +45,4 @@ initialconditionf = "PATH/TO/FILE"
 networkf = "PATH/TO/FILE"
 rssarn = loadrxnetwork(RSSANetwork(), "RSSARxSys", initialconditionf, networkf)
 ```
-Here `RSSANetwork` specifies the type of the file to parse, and `RSSARxSys` gives the type of the generated `min_reaction_network`. `rssarn` is again a `ParsedReactionNetwork`, but only the `rn`, `u₀` and `rnstr` fields will now be relevant (the remaining fields will be set to `nothing`).
+Here `RSSANetwork` specifies the type of the file to parse, and `RSSARxSys` gives the type of the generated `reaction_network`. `rssarn` is again a `ParsedReactionNetwork`, but only the `rn` and `u₀` fields will now be relevant (the remaining fields will be set to `nothing`).

src/parsing_routines_rssafiles.jl

@@ -73,5 +73,5 @@ function loadrxnetwork(ft::RSSANetwork, networkname, specs_ic_file, rxs_file; kw
     rn,rnstr = build_rxnetwork(ft, networkname, rxstrs, rxrates; kwargs...)
     initialpop = get_init_condit(ft, rn, specs_ic)
 
-    ParsedReactionNetwork(rn, initialpop; rnstr=rnstr)
+    ParsedReactionNetwork(rn, initialpop)
 end