build based on f938c8c4

32733d0f · Documenter.jl · fac57361 · 32733d0f · 32733d0f · 32733d0f
Commit 32733d0f authored Apr 13, 2021 by Documenter.jl
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-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · SBML.jl</title><link rel="canonical" href="https://lcsb-biocore.github.io/DistributedData.jl/stable/search/"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="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><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="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><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../"><img src="../assets/logo.svg" alt="SBML.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit">SBML.jl</span></div><form class="docs-search" action><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Documentation</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Tuesday 13 April 2021 12:59">Tuesday 13 April 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Search · SBML.jl</title><link rel="canonical" href="https://lcsb-biocore.github.io/DistributedData.jl/stable/search/"/><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="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><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="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><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../"><img src="../assets/logo.svg" alt="SBML.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit">SBML.jl</span></div><form class="docs-search" action><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Documentation</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Search</a></li></ul></nav><div class="docs-right"><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Tuesday 13 April 2021 13:01">Tuesday 13 April 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="../search_index.js"></script><script src="../assets/search.js"></script></html>
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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). 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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"}]
 }