Commit 86460503 authored by Documenter.jl's avatar Documenter.jl
Browse files

build based on 08ffba87

parent c6836f8c
......@@ -26,7 +26,7 @@ julia> S
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
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
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
⋮ ⋮ ⋱ ⋮ ⋮ </code></pre><h2 id="Functions"><a class="docs-heading-anchor" href="#Functions">Functions</a><a id="Functions-1"></a><a class="docs-heading-anchor-permalink" href="#Functions" title="Permalink"></a></h2><h3 id="Data-structures"><a class="docs-heading-anchor" href="#Data-structures">Data structures</a><a id="Data-structures-1"></a><a class="docs-heading-anchor-permalink" href="#Data-structures" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="SBML.Model" href="#SBML.Model"><code>SBML.Model</code></a><span class="docstring-category">Type</span></header><section><div><p>Structure that collects the model-related data. Contains <code>units</code>, <code>compartments</code>, <code>species</code> and <code>reactions</code>. The contained dictionaries are indexed by identifiers of the corresponding objects.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/structs.jl#L47-L51">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Reaction" href="#SBML.Reaction"><code>SBML.Reaction</code></a><span class="docstring-category">Type</span></header><section><div><p>Reaction with stoichiometry that assigns reactants and products their relative consumption/production rates (accessible in field <code>stoichiometry</code>), lower/upper bounds (in tuples <code>lb</code> and <code>ub</code>, with unit names), and objective coefficient (<code>oc</code>).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/structs.jl#L23-L28">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Species" href="#SBML.Species"><code>SBML.Species</code></a><span class="docstring-category">Type</span></header><section><div><p>Species metadata – contains a human-readable <code>name</code>, and a <code>compartment</code> identifier</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/structs.jl#L37-L40">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.UnitPart" href="#SBML.UnitPart"><code>SBML.UnitPart</code></a><span class="docstring-category">Type</span></header><section><div><p>Part of a measurement unit definition that corresponds to the SBML definition of <code>Unit</code>. For example, the unit &quot;per square megahour&quot;, Mh^(-2), is written as:</p><pre><code class="language-none">UnitPart(&quot;second&quot;, # base SI unit, this says we are measuring time
⋮ ⋮ ⋱ ⋮ ⋮ </code></pre><h2 id="Functions"><a class="docs-heading-anchor" href="#Functions">Functions</a><a id="Functions-1"></a><a class="docs-heading-anchor-permalink" href="#Functions" title="Permalink"></a></h2><h3 id="Data-structures"><a class="docs-heading-anchor" href="#Data-structures">Data structures</a><a id="Data-structures-1"></a><a class="docs-heading-anchor-permalink" href="#Data-structures" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="SBML.Model" href="#SBML.Model"><code>SBML.Model</code></a><span class="docstring-category">Type</span></header><section><div><p>Structure that collects the model-related data. Contains <code>units</code>, <code>compartments</code>, <code>species</code> and <code>reactions</code>. The contained dictionaries are indexed by identifiers of the corresponding objects.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/structs.jl#L47-L51">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Reaction" href="#SBML.Reaction"><code>SBML.Reaction</code></a><span class="docstring-category">Type</span></header><section><div><p>Reaction with stoichiometry that assigns reactants and products their relative consumption/production rates (accessible in field <code>stoichiometry</code>), lower/upper bounds (in tuples <code>lb</code> and <code>ub</code>, with unit names), and objective coefficient (<code>oc</code>).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/structs.jl#L23-L28">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Species" href="#SBML.Species"><code>SBML.Species</code></a><span class="docstring-category">Type</span></header><section><div><p>Species metadata – contains a human-readable <code>name</code>, and a <code>compartment</code> identifier</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/structs.jl#L37-L40">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.UnitPart" href="#SBML.UnitPart"><code>SBML.UnitPart</code></a><span class="docstring-category">Type</span></header><section><div><p>Part of a measurement unit definition that corresponds to the SBML definition of <code>Unit</code>. For example, the unit &quot;per square megahour&quot;, Mh^(-2), is written as:</p><pre><code class="language-none">UnitPart(&quot;second&quot;, # base SI unit, this says we are measuring time
-2, # exponent, says &quot;per square&quot;
6, # log-10 scale of the unit, says &quot;mega&quot;
1/3600) # second-to-hour multiplier</code></pre><p>Compound units (such as &quot;volt-amperes&quot; and &quot;dozens of yards per ounce&quot;) are built from multiple <code>UnitPart</code>s; see the definition of field <code>units</code> in <a href="#SBML.Model"><code>Model</code></a>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/structs.jl#L2-L14">source</a></section></article><h3 id="Base-functions"><a class="docs-heading-anchor" href="#Base-functions">Base functions</a><a id="Base-functions-1"></a><a class="docs-heading-anchor-permalink" href="#Base-functions" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="SBML.SBMLVersion-Tuple{}" href="#SBML.SBMLVersion-Tuple{}"><code>SBML.SBMLVersion</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function SBMLVersion()</code></pre><p>Get the version of the used SBML library in Julia version format.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/version.jl#L2-L6">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.readSBML-Tuple{String}" href="#SBML.readSBML-Tuple{String}"><code>SBML.readSBML</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function readSBML(fn::String)::Model</code></pre><p>Read the SBML from a XML file in <code>fn</code> and return the contained <code>Model</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/readsbml.jl#L4-L8">source</a></section></article><h2 id="Data-helpers"><a class="docs-heading-anchor" href="#Data-helpers">Data helpers</a><a id="Data-helpers-1"></a><a class="docs-heading-anchor-permalink" href="#Data-helpers" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="SBML.getLBs-Tuple{Model}" href="#SBML.getLBs-Tuple{Model}"><code>SBML.getLBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getLBs(m::Model)::Vector{Tuple{Float64,String}}</code></pre><p>Extract 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).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/utils.jl#L20-L26">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getOCs-Tuple{Model}" href="#SBML.getOCs-Tuple{Model}"><code>SBML.getOCs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getOCs(m::Model)::Vector{Float64}</code></pre><p>Extract the vector of objective coefficients of each reaction.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/utils.jl#L40-L44">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getS-Tuple{Model}" href="#SBML.getS-Tuple{Model}"><code>SBML.getS</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getS(m::Model)::Tuple{Vector{String},Vector{String},Matrix{Float64}}</code></pre><p>Extract the vector of species (aka metabolite) identifiers, vector of reaction identifiers, and the (dense) stoichiometry matrix from an existing <code>Model</code>. Returns a tuple with these values.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/utils.jl#L1-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getUBs-Tuple{Model}" href="#SBML.getUBs-Tuple{Model}"><code>SBML.getUBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getUBs(m::Model)::Vector{Tuple{Float64,String}}</code></pre><p>Likewise to <code>getLBs</code>, extract the upper bounds.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/83412adb82355e0444606a6003e9583a5e1d76d2/src/utils.jl#L31-L35">source</a></section></article></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="Monday 15 February 2021 07:55">Monday 15 February 2021</span>. Using Julia version 1.5.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
1/3600) # second-to-hour multiplier</code></pre><p>Compound units (such as &quot;volt-amperes&quot; and &quot;dozens of yards per ounce&quot;) are built from multiple <code>UnitPart</code>s; see the definition of field <code>units</code> in <a href="#SBML.Model"><code>Model</code></a>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/structs.jl#L2-L14">source</a></section></article><h3 id="Base-functions"><a class="docs-heading-anchor" href="#Base-functions">Base functions</a><a id="Base-functions-1"></a><a class="docs-heading-anchor-permalink" href="#Base-functions" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="SBML.SBMLVersion-Tuple{}" href="#SBML.SBMLVersion-Tuple{}"><code>SBML.SBMLVersion</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function SBMLVersion()</code></pre><p>Get the version of the used SBML library in Julia version format.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/version.jl#L2-L6">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.readSBML-Tuple{String}" href="#SBML.readSBML-Tuple{String}"><code>SBML.readSBML</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function readSBML(fn::String)::Model</code></pre><p>Read the SBML from a XML file in <code>fn</code> and return the contained <code>Model</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/readsbml.jl#L4-L8">source</a></section></article><h2 id="Data-helpers"><a class="docs-heading-anchor" href="#Data-helpers">Data helpers</a><a id="Data-helpers-1"></a><a class="docs-heading-anchor-permalink" href="#Data-helpers" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="SBML.getLBs-Tuple{Model}" href="#SBML.getLBs-Tuple{Model}"><code>SBML.getLBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getLBs(m::Model)::Vector{Tuple{Float64,String}}</code></pre><p>Extract 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).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/utils.jl#L20-L26">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getOCs-Tuple{Model}" href="#SBML.getOCs-Tuple{Model}"><code>SBML.getOCs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getOCs(m::Model)::Vector{Float64}</code></pre><p>Extract the vector of objective coefficients of each reaction.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/utils.jl#L40-L44">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getS-Tuple{Model}" href="#SBML.getS-Tuple{Model}"><code>SBML.getS</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getS(m::Model)::Tuple{Vector{String},Vector{String},Matrix{Float64}}</code></pre><p>Extract the vector of species (aka metabolite) identifiers, vector of reaction identifiers, and the (dense) stoichiometry matrix from an existing <code>Model</code>. Returns a tuple with these values.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/utils.jl#L1-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getUBs-Tuple{Model}" href="#SBML.getUBs-Tuple{Model}"><code>SBML.getUBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getUBs(m::Model)::Vector{Tuple{Float64,String}}</code></pre><p>Likewise to <code>getLBs</code>, extract the upper bounds.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/08ffba8771a91a311baed0e90a9ad7517c6d6e8f/src/utils.jl#L31-L35">source</a></section></article></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="Wednesday 24 February 2021 06:15">Wednesday 24 February 2021</span>. Using Julia version 1.5.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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