diff --git a/README.md b/README.md index 252e8a7..f928542 100644 --- a/README.md +++ b/README.md @@ -52,7 +52,7 @@ Here `BNGNetwork` is a type specifying the file format that is being loaded. `prnbng` is a `ParsedReactionNetwork` structure with the following fields: - `rn`, a Catalyst `ReactionSystem` - - `u₀`, a `Dict` mapping initial condition symbolic variables to numeric values + - `u0`, a `Dict` mapping initial condition symbolic variables to numeric values and/or symbolic expressions. - `p`, a `Dict` mapping parameter symbolic variables to numeric values and/or symbolic expressions. @@ -221,4 +221,4 @@ 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 `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`). --> +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`). --> diff --git a/docs/src/index.md b/docs/src/index.md index 2452885..af3106c 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -64,7 +64,7 @@ Here `BNGNetwork` is a type specifying the file format that is being loaded. `prnbng` is a `ParsedReactionNetwork` structure with the following fields: - `rn`, a Catalyst `ReactionSystem` - - `u₀`, a `Dict` mapping initial condition symbolic variables to numeric values + - `u0`, a `Dict` mapping initial condition symbolic variables to numeric values and/or symbolic expressions. - `p`, a `Dict` mapping parameter symbolic variables to numeric values and/or symbolic expressions. diff --git a/src/ReactionNetworkImporters.jl b/src/ReactionNetworkImporters.jl index 645e97f..e0657c8 100644 --- a/src/ReactionNetworkImporters.jl +++ b/src/ReactionNetworkImporters.jl @@ -24,7 +24,7 @@ struct ParsedReactionNetwork rn::ReactionSystem "Dict mapping initial condition symbolic variables to values." - u₀::Any + u0::Any "Dict mapping parameter symbolic variables to values." p::Any @@ -35,9 +35,9 @@ struct ParsedReactionNetwork "Dict from group name (as string) to corresponding symbolic variable" groupstosyms::Any end -function ParsedReactionNetwork(rn::ReactionSystem; u₀ = nothing, p = nothing, +function ParsedReactionNetwork(rn::ReactionSystem; u0 = nothing, p = nothing, varstonames = nothing, groupstosyms = nothing) - ParsedReactionNetwork(rn, u₀, p, varstonames, groupstosyms) + ParsedReactionNetwork(rn, u0, p, varstonames, groupstosyms) end export BNGNetwork, MatrixNetwork, ParsedReactionNetwork, ComplexMatrixNetwork