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<htmllang="en"><head><metacharset="UTF-8"/><metaname="viewport"content="width=device-width, initial-scale=1.0"/><title>Search · SBML.jl</title><linkrel="canonical"href="https://lcsb-biocore.github.io/DistributedData.jl/stable/search/"/><linkhref="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono"rel="stylesheet"type="text/css"/><linkhref="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css"rel="stylesheet"type="text/css"/><linkhref="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css"rel="stylesheet"type="text/css"/><linkhref="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css"rel="stylesheet"type="text/css"/><linkhref="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/katex.min.css"rel="stylesheet"type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js"data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><linkclass="docs-theme-link"rel="stylesheet"type="text/css"href="../assets/themes/documenter-dark.css"data-theme-name="documenter-dark"data-theme-primary-dark/><linkclass="docs-theme-link"rel="stylesheet"type="text/css"href="../assets/themes/documenter-light.css"data-theme-name="documenter-light"data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><divid="documenter"><navclass="docs-sidebar"><aclass="docs-logo"href="../"><imgsrc="../assets/logo.svg"alt="SBML.jl logo"/></a><divclass="docs-package-name"><spanclass="docs-autofit">SBML.jl</span></div><formclass="docs-search"action><inputclass="docs-search-query"id="documenter-search-query"name="q"type="text"placeholder="Search docs"/></form><ulclass="docs-menu"><li><aclass="tocitem"href="../">Documentation</a></li></ul><divclass="docs-version-selector field has-addons"><divclass="control"><spanclass="docs-label button is-static is-size-7">Version</span></div><divclass="docs-selector control is-expanded"><divclass="select is-fullwidth is-size-7"><selectid="documenter-version-selector"></select></div></div></div></nav><divclass="docs-main"><headerclass="docs-navbar"><navclass="breadcrumb"><ulclass="is-hidden-mobile"><liclass="is-active"><ahref>Search</a></li></ul><ulclass="is-hidden-tablet"><liclass="is-active"><ahref>Search</a></li></ul></nav><divclass="docs-right"><aclass="docs-settings-button fas fa-cog"id="documenter-settings-button"href="#"title="Settings"></a><aclass="docs-sidebar-button fa fa-bars is-hidden-desktop"id="documenter-sidebar-button"href="#"></a></div></header><article><pid="documenter-search-info">Loading search...</p><ulid="documenter-search-results"></ul></article><navclass="docs-footer"><pclass="footer-message">Powered by <ahref="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <ahref="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><divclass="modal"id="documenter-settings"><divclass="modal-background"></div><divclass="modal-card"><headerclass="modal-card-head"><pclass="modal-card-title">Settings</p><buttonclass="delete"></button></header><sectionclass="modal-card-body"><p><labelclass="label">Theme</label><divclass="select"><selectid="documenter-themepicker"><optionvalue="documenter-light">documenter-light</option><optionvalue="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <ahref="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <spanclass="colophon-date"title="Tuesday 13 April 2021 13:01">Tuesday 13 April 2021</span>. Using Julia version 1.5.4.</p></section><footerclass="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>
[{"location":"#SBML.jl-—-load-systems-biology-models-from-SBML-files","page":"Documentation","title":"SBML.jl — load systems biology models from SBML files","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"This package provides a straightforward way to load model- and simulation-relevant information from SBML files.","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"The library provides a single function readSBML to load a Model:","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"julia> using SBML\njulia> mdl = readSBML(\"Ec_core_flux1.xml\")\nModel(…)\n\njulia> mdl.compartments\n2-element Array{String,1}:\n\"Extra_organism\"\n\"Cytosol\"","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"There are several functions to help you with using the data in the usual COBRA-style workflows, such as getS:","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"julia> metabolites, reactions, S = getS(mdl)\njulia> metabolites\n77-element Array{String,1}:\n\"M_succoa_c\"\n\"M_ac_c\"\n\"M_etoh_c\"\n ⋮\n\njulia> S\n77×77 SparseArrays.SparseMatrixCSC{Float64,Int64} with 308 stored entries:\n [60, 1] = -1.0\n [68, 1] = 1.0\n [1 , 2] = 1.0\n [6 , 2] = -1.0\n ⋮\n [23, 76] = 1.0\n [56, 76] = -1.0\n [30, 77] = -1.0\n [48, 77] = 1.0\n\njulia> Matrix(S)\n77×77 Array{Float64,2}:\n 0.0 1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 -1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 -1.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0\n ⋮ ⋮ ⋱ ⋮ ⋮ ","category":"page"},{"location":"#Functions","page":"Documentation","title":"Functions","text":"","category":"section"},{"location":"#Data-structures","page":"Documentation","title":"Data structures","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"Modules = [SBML]\nPages = [\"structs.jl\"]","category":"page"},{"location":"#SBML.Maybe","page":"Documentation","title":"SBML.Maybe","text":"Maybe{X}\n\nType shortcut for \"X or nothing\" or \"nullable X\" in javaspeak. Name got inspired by our functional friends.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GPAAnd","page":"Documentation","title":"SBML.GPAAnd","text":"Boolean binary \"and\" in the association expression\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GPAOr","page":"Documentation","title":"SBML.GPAOr","text":"Boolean binary \"or\" in the association expression\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GPARef","page":"Documentation","title":"SBML.GPARef","text":"Gene product reference in the association expression\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GeneProduct","page":"Documentation","title":"SBML.GeneProduct","text":"Gene product metadata.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GeneProductAssociation","page":"Documentation","title":"SBML.GeneProductAssociation","text":"Abstract type for all kinds of gene product associations\n\n\n\n\n\n","category":"type"},{"location":"#SBML.Model","page":"Documentation","title":"SBML.Model","text":"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.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.Reaction","page":"Documentation","title":"SBML.Reaction","text":"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.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.Species","page":"Documentation","title":"SBML.Species","text":"Species metadata – contains a human-readable name, a compartment identifier, formula, charge, and additional notes and annotation.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.UnitPart","page":"Documentation","title":"SBML.UnitPart","text":"Part of a measurement unit definition that corresponds to the SBML definition of Unit. For example, the unit \"per square megahour\", Mh^(-2), is written as:\n\nUnitPart(\"second\", # base SI unit, this says we are measuring time\n -2, # exponent, says \"per square\"\n 6, # log-10 scale of the unit, says \"mega\"\n 1/3600) # second-to-hour multiplier\n\nCompound units (such as \"volt-amperes\" and \"dozens of yards per ounce\") are built from multiple UnitParts; see the definition of field units in Model.\n\n\n\n\n\n","category":"type"},{"location":"#Base-functions","page":"Documentation","title":"Base functions","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"Modules = [SBML]\nPages = [\"version.jl\", \"readsbml.jl\"]","category":"page"},{"location":"#SBML.SBMLVersion-Tuple{}","page":"Documentation","title":"SBML.SBMLVersion","text":"function SBMLVersion()\n\nGet the version of the used SBML library in Julia version format.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.extractModel-Tuple{Ptr{Nothing}}","page":"Documentation","title":"SBML.extractModel","text":"\" function extractModel(mdl::VPtr)::Model\n\nTake the SBMLModel_t pointer and extract all information required to make a valid Model structure.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getAssociation-Tuple{Ptr{Nothing}}","page":"Documentation","title":"SBML.getAssociation","text":"function getAssociation(x::VPtr)::GeneProductAssociation\n\nConvert a pointer to SBML FbcAssociation_t to the GeneProductAssociation tree structure.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getOptionalString-Tuple{Ptr{Nothing},Any}","page":"Documentation","title":"SBML.getOptionalString","text":"function getOptionalString(x::VPtr, fn_sym)::Maybe{String}\n\nC-call the SBML function fn_sym with a single parameter x, interpret the result as a nullable string pointer and return appropriately.\n\nThis is used to get notes and annotations and several other things (see getNotes, getAnnotations)\n\n\n\n\n\n","category":"method"},{"location":"#SBML.readSBML-Tuple{String}","page":"Documentation","title":"SBML.readSBML","text":"function readSBML(fn::String)::Model\n\nRead the SBML from a XML file in fn and return the contained Model.\n\n\n\n\n\n","category":"method"},{"location":"#Data-helpers","page":"Documentation","title":"Data helpers","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"Modules = [SBML]\nPages = [\"utils.jl\"]","category":"page"},{"location":"#SBML.getLBs-Tuple{Model}","page":"Documentation","title":"SBML.getLBs","text":"function getLBs(m::Model)::Vector{Tuple{Float64,String}}\n\nExtract a vector of lower bounds of reaction rates from the model. All bounds are accompanied with the unit of the corresponding value (this behavior is based on SBML specification).\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getOCs-Tuple{Model}","page":"Documentation","title":"SBML.getOCs","text":"function getOCs(m::Model)::Vector{Float64}\n\nExtract the vector of objective coefficients of each reaction.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getS-Tuple{Model}","page":"Documentation","title":"SBML.getS","text":"function getS(m::Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{Float64}}\n\nExtract the vector of species (aka metabolite) identifiers, vector of reaction identifiers, and the (dense) stoichiometry matrix from an existing Model. Returns a tuple with these values.\n\nThe matrix is sparse by default (initially constructed by SparseArrays.spzeros). You can fill in a custom empty matrix constructed to argument zeros; e.g. running with zeros=zeros will produce a dense matrix.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getUBs-Tuple{Model}","page":"Documentation","title":"SBML.getUBs","text":"function getUBs(m::Model)::Vector{Tuple{Float64,String}}\n\nLikewise to getLBs, extract the upper bounds.\n\n\n\n\n\n","category":"method"}]
[{"location":"#SBML.jl-—-load-systems-biology-models-from-SBML-files","page":"Documentation","title":"SBML.jl — load systems biology models from SBML files","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"This package provides a straightforward way to load model- and simulation-relevant information from SBML files.","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"The library provides a single function readSBML to load a Model:","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"julia> using SBML\njulia> mdl = readSBML(\"Ec_core_flux1.xml\")\nModel(…)\n\njulia> mdl.compartments\n2-element Array{String,1}:\n\"Extra_organism\"\n\"Cytosol\"","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"There are several functions to help you with using the data in the usual COBRA-style workflows, such as getS:","category":"page"},{"location":"","page":"Documentation","title":"Documentation","text":"julia> metabolites, reactions, S = getS(mdl)\njulia> metabolites\n77-element Array{String,1}:\n\"M_succoa_c\"\n\"M_ac_c\"\n\"M_etoh_c\"\n ⋮\n\njulia> S\n77×77 SparseArrays.SparseMatrixCSC{Float64,Int64} with 308 stored entries:\n [60, 1] = -1.0\n [68, 1] = 1.0\n [1 , 2] = 1.0\n [6 , 2] = -1.0\n ⋮\n [23, 76] = 1.0\n [56, 76] = -1.0\n [30, 77] = -1.0\n [48, 77] = 1.0\n\njulia> Matrix(S)\n77×77 Array{Float64,2}:\n 0.0 1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 -1.0 0.0 0.0 0.0 0.0 0.0 … 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 -1.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0\n 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -1.0 0.0 0.0 0.0 0.0 0.0\n ⋮ ⋮ ⋱ ⋮ ⋮ ","category":"page"},{"location":"#Functions","page":"Documentation","title":"Functions","text":"","category":"section"},{"location":"#Data-structures","page":"Documentation","title":"Data structures","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"Modules = [SBML]\nPages = [\"structs.jl\"]","category":"page"},{"location":"#SBML.Maybe","page":"Documentation","title":"SBML.Maybe","text":"Maybe{X}\n\nType shortcut for \"X or nothing\" or \"nullable X\" in javaspeak. Name got inspired by our functional friends.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GPAAnd","page":"Documentation","title":"SBML.GPAAnd","text":"Boolean binary \"and\" in the association expression\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GPAOr","page":"Documentation","title":"SBML.GPAOr","text":"Boolean binary \"or\" in the association expression\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GPARef","page":"Documentation","title":"SBML.GPARef","text":"Gene product reference in the association expression\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GeneProduct","page":"Documentation","title":"SBML.GeneProduct","text":"Gene product metadata.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.GeneProductAssociation","page":"Documentation","title":"SBML.GeneProductAssociation","text":"Abstract type for all kinds of gene product associations\n\n\n\n\n\n","category":"type"},{"location":"#SBML.Model","page":"Documentation","title":"SBML.Model","text":"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.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.Reaction","page":"Documentation","title":"SBML.Reaction","text":"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.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.Species","page":"Documentation","title":"SBML.Species","text":"Species metadata – contains a human-readable name, a compartment identifier, formula, charge, and additional notes and annotation.\n\n\n\n\n\n","category":"type"},{"location":"#SBML.UnitPart","page":"Documentation","title":"SBML.UnitPart","text":"Part of a measurement unit definition that corresponds to the SBML definition of Unit. For example, the unit \"per square megahour\", Mh^(-2), is written as:\n\nUnitPart(\"second\", # base SI unit, this says we are measuring time\n -2, # exponent, says \"per square\"\n 6, # log-10 scale of the unit, says \"mega\"\n 1/3600) # second-to-hour multiplier\n\nCompound units (such as \"volt-amperes\" and \"dozens of yards per ounce\") are built from multiple UnitParts; see the definition of field units in Model.\n\n\n\n\n\n","category":"type"},{"location":"#Base-functions","page":"Documentation","title":"Base functions","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"Modules = [SBML]\nPages = [\"version.jl\", \"readsbml.jl\"]","category":"page"},{"location":"#SBML.SBMLVersion-Tuple{}","page":"Documentation","title":"SBML.SBMLVersion","text":"function SBMLVersion()\n\nGet the version of the used SBML library in Julia version format.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.extractModel-Tuple{Ptr{Nothing}}","page":"Documentation","title":"SBML.extractModel","text":"\" function extractModel(mdl::VPtr)::Model\n\nTake the SBMLModel_t pointer and extract all information required to make a valid Model structure.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getAssociation-Tuple{Ptr{Nothing}}","page":"Documentation","title":"SBML.getAssociation","text":"function getAssociation(x::VPtr)::GeneProductAssociation\n\nConvert a pointer to SBML FbcAssociation_t to the GeneProductAssociation tree structure.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.get_optional_string-Tuple{Ptr{Nothing},Any}","page":"Documentation","title":"SBML.get_optional_string","text":"function get_optional_string(x::VPtr, fn_sym)::Maybe{String}\n\nLike get_string, but returns nothing instead of throwing an exception.\n\nThis is used to get notes and annotations and several other things (see getNotes, getAnnotations)\n\n\n\n\n\n","category":"method"},{"location":"#SBML.get_string-Tuple{Ptr{Nothing},Any}","page":"Documentation","title":"SBML.get_string","text":"function get_string(x::VPtr, fn_sym)::Maybe{String}\n\nC-call the SBML function fn_sym with a single parameter x, interpret the result as a string and return it, or throw exception in case the pointer is NULL.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.readSBML-Tuple{String}","page":"Documentation","title":"SBML.readSBML","text":"function readSBML(fn::String)::Model\n\nRead the SBML from a XML file in fn and return the contained Model.\n\n\n\n\n\n","category":"method"},{"location":"#Data-helpers","page":"Documentation","title":"Data helpers","text":"","category":"section"},{"location":"","page":"Documentation","title":"Documentation","text":"Modules = [SBML]\nPages = [\"utils.jl\"]","category":"page"},{"location":"#SBML.getLBs-Tuple{Model}","page":"Documentation","title":"SBML.getLBs","text":"function getLBs(m::Model)::Vector{Tuple{Float64,String}}\n\nExtract a vector of lower bounds of reaction rates from the model. All bounds are accompanied with the unit of the corresponding value (this behavior is based on SBML specification).\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getOCs-Tuple{Model}","page":"Documentation","title":"SBML.getOCs","text":"function getOCs(m::Model)::Vector{Float64}\n\nExtract the vector of objective coefficients of each reaction.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getS-Tuple{Model}","page":"Documentation","title":"SBML.getS","text":"function getS(m::Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{Float64}}\n\nExtract the vector of species (aka metabolite) identifiers, vector of reaction identifiers, and the (dense) stoichiometry matrix from an existing Model. Returns a tuple with these values.\n\nThe matrix is sparse by default (initially constructed by SparseArrays.spzeros). You can fill in a custom empty matrix constructed to argument zeros; e.g. running with zeros=zeros will produce a dense matrix.\n\n\n\n\n\n","category":"method"},{"location":"#SBML.getUBs-Tuple{Model}","page":"Documentation","title":"SBML.getUBs","text":"function getUBs(m::Model)::Vector{Tuple{Float64,String}}\n\nLikewise to getLBs, extract the upper bounds.\n\n\n\n\n\n","category":"method"}]