Commit 6b49d8f7 authored by anand jain's avatar anand jain
Browse files

docstringextensions

parent 4ef5b4b3
......@@ -4,6 +4,7 @@ authors = ["Mirek Kratochvil <miroslav.kratochvil@uni.lu>", "LCSB R3 team <lcsb-
version = "0.6.0"
[deps]
DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
SBML_jll = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1"
......
"""
$(DocStringExtensions.README)
"""
module SBML
using DocStringExtensions
using SBML_jll, Libdl
using SparseArrays
using Symbolics
......
......@@ -77,7 +77,12 @@ struct MathLambda <: Math
end
"""
$(TYPEDEF)
SBML Compartment with sizing information.
# Fields
$(FIELDS)
"""
struct Compartment
name::Maybe{String}
......@@ -91,10 +96,15 @@ struct Compartment
end
"""
$(TYPEDEF)
Reaction with stoichiometry that assigns reactants and products their relative
consumption/production rates (accessible in field `stoichiometry`), lower/upper
bounds (in tuples `lb` and `ub`, with unit names), and objective coefficient
(`oc`). Also may contains `notes` and `annotation`.
# Fields
$(FIELDS)
"""
struct Reaction
stoichiometry::Dict{String,Float64}
......@@ -111,8 +121,13 @@ struct Reaction
end
"""
$(TYPEDEF)
Species metadata -- contains a human-readable `name`, a `compartment`
identifier, `formula`, `charge`, and additional `notes` and `annotation`.
# Fields
$(FIELDS)
"""
struct Species
name::Maybe{String}
......@@ -130,7 +145,12 @@ struct Species
end
"""
$(TYPEDEF)
Gene product metadata.
# Fields
$(FIELDS)
"""
struct GeneProduct
name::Maybe{String}
......@@ -152,11 +172,16 @@ struct FunctionDefinition
end
"""
$(TYPEDEF)
Structure that collects the model-related data. Contains `parameters`, `units`,
`compartments`, `species` and `reactions` and `gene_products`, and additional
`notes` and `annotation` (also present internally in some of the data fields).
The contained dictionaries are indexed by identifiers of the corresponding
objects.
# Fields
$(FIELDS)
"""
struct Model
parameters::Dict{String,Float64}
......
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