Commit 54cb264b authored by Documenter.jl's avatar Documenter.jl
Browse files

build based on 41a25d0d

parent f0021c05
......@@ -38,15 +38,15 @@ julia> Matrix(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><h1 id="Function-reference"><a class="docs-heading-anchor" href="#Function-reference">Function reference</a><a id="Function-reference-1"></a><a class="docs-heading-anchor-permalink" href="#Function-reference" title="Permalink"></a></h1><h2 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></h2><article class="docstring"><header><a class="docstring-binding" id="SBML.Maybe" href="#SBML.Maybe"><code>SBML.Maybe</code></a><span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia">Maybe{X}</code></pre><p>Type shortcut for &quot;<code>X</code> or nothing&quot; or &quot;nullable <code>X</code>&quot; in javaspeak. Name got inspired by our functional friends.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L2-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Compartment" href="#SBML.Compartment"><code>SBML.Compartment</code></a><span class="docstring-category">Type</span></header><section><div><p>SBML Compartment with sizing information.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L109-L111">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.FunctionDefinition" href="#SBML.FunctionDefinition"><code>SBML.FunctionDefinition</code></a><span class="docstring-category">Type</span></header><section><div><p>Custom function definition.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L173-L175">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GPAAnd" href="#SBML.GPAAnd"><code>SBML.GPAAnd</code></a><span class="docstring-category">Type</span></header><section><div><p>Boolean binary &quot;and&quot; in the association expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L44-L46">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GPAOr" href="#SBML.GPAOr"><code>SBML.GPAOr</code></a><span class="docstring-category">Type</span></header><section><div><p>Boolean binary &quot;or&quot; in the association expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L51-L53">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GPARef" href="#SBML.GPARef"><code>SBML.GPARef</code></a><span class="docstring-category">Type</span></header><section><div><p>Gene product reference in the association expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L37-L39">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GeneProduct" href="#SBML.GeneProduct"><code>SBML.GeneProduct</code></a><span class="docstring-category">Type</span></header><section><div><p>Gene product metadata.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L162-L164">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GeneProductAssociation" href="#SBML.GeneProductAssociation"><code>SBML.GeneProductAssociation</code></a><span class="docstring-category">Type</span></header><section><div><p>Abstract type for all kinds of gene product associations</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L32-L34">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Math" href="#SBML.Math"><code>SBML.Math</code></a><span class="docstring-category">Type</span></header><section><div><p>A simplified representation of MathML-specified math AST</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L58-L60">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathApply" href="#SBML.MathApply"><code>SBML.MathApply</code></a><span class="docstring-category">Type</span></header><section><div><p>Function application (&quot;call by name&quot;, no tricks allowed) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L93-L95">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathConst" href="#SBML.MathConst"><code>SBML.MathConst</code></a><span class="docstring-category">Type</span></header><section><div><p>A constant identified by name (usually something like <code>pi</code>, <code>e</code> or <code>true</code>) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L77-L80">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathIdent" href="#SBML.MathIdent"><code>SBML.MathIdent</code></a><span class="docstring-category">Type</span></header><section><div><p>An identifier (usually a variable name) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L70-L72">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathLambda" href="#SBML.MathLambda"><code>SBML.MathLambda</code></a><span class="docstring-category">Type</span></header><section><div><p>Function definition (aka &quot;lambda&quot;) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L101-L103">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathTime" href="#SBML.MathTime"><code>SBML.MathTime</code></a><span class="docstring-category">Type</span></header><section><div><p>A special value representing the current time of the simulation, with a special name.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L85-L88">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathVal" href="#SBML.MathVal"><code>SBML.MathVal</code></a><span class="docstring-category">Type</span></header><section><div><p>A literal value (usually a numeric constant) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L63-L65">source</a></section></article><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>parameters</code>, <code>units</code>, <code>compartments</code>, <code>species</code> and <code>reactions</code> and <code>gene_products</code>, and additional <code>notes</code> and <code>annotation</code> (also present internally in some of the data fields). 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/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L184-L190">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>). Also may contains <code>notes</code> and <code>annotation</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L123-L128">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>, a <code>compartment</code> identifier, <code>formula</code>, <code>charge</code>, and additional <code>notes</code> and <code>annotation</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L143-L146">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="nohighlight">SBML.UnitPart(&quot;second&quot;, # base SI unit, this says we are measuring time
⋮ ⋮ ⋱ ⋮ ⋮ </code></pre><h1 id="Function-reference"><a class="docs-heading-anchor" href="#Function-reference">Function reference</a><a id="Function-reference-1"></a><a class="docs-heading-anchor-permalink" href="#Function-reference" title="Permalink"></a></h1><h2 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></h2><article class="docstring"><header><a class="docstring-binding" id="SBML.Maybe" href="#SBML.Maybe"><code>SBML.Maybe</code></a><span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia">Maybe{X}</code></pre><p>Type shortcut for &quot;<code>X</code> or nothing&quot; or &quot;nullable <code>X</code>&quot; in javaspeak. Name got inspired by our functional friends.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L2-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Compartment" href="#SBML.Compartment"><code>SBML.Compartment</code></a><span class="docstring-category">Type</span></header><section><div><p>SBML Compartment with sizing information.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L109-L111">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.FunctionDefinition" href="#SBML.FunctionDefinition"><code>SBML.FunctionDefinition</code></a><span class="docstring-category">Type</span></header><section><div><p>Custom function definition.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L173-L175">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GPAAnd" href="#SBML.GPAAnd"><code>SBML.GPAAnd</code></a><span class="docstring-category">Type</span></header><section><div><p>Boolean binary &quot;and&quot; in the association expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L44-L46">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GPAOr" href="#SBML.GPAOr"><code>SBML.GPAOr</code></a><span class="docstring-category">Type</span></header><section><div><p>Boolean binary &quot;or&quot; in the association expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L51-L53">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GPARef" href="#SBML.GPARef"><code>SBML.GPARef</code></a><span class="docstring-category">Type</span></header><section><div><p>Gene product reference in the association expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L37-L39">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GeneProduct" href="#SBML.GeneProduct"><code>SBML.GeneProduct</code></a><span class="docstring-category">Type</span></header><section><div><p>Gene product metadata.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L162-L164">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.GeneProductAssociation" href="#SBML.GeneProductAssociation"><code>SBML.GeneProductAssociation</code></a><span class="docstring-category">Type</span></header><section><div><p>Abstract type for all kinds of gene product associations</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L32-L34">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.Math" href="#SBML.Math"><code>SBML.Math</code></a><span class="docstring-category">Type</span></header><section><div><p>A simplified representation of MathML-specified math AST</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L58-L60">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathApply" href="#SBML.MathApply"><code>SBML.MathApply</code></a><span class="docstring-category">Type</span></header><section><div><p>Function application (&quot;call by name&quot;, no tricks allowed) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L93-L95">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathConst" href="#SBML.MathConst"><code>SBML.MathConst</code></a><span class="docstring-category">Type</span></header><section><div><p>A constant identified by name (usually something like <code>pi</code>, <code>e</code> or <code>true</code>) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L77-L80">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathIdent" href="#SBML.MathIdent"><code>SBML.MathIdent</code></a><span class="docstring-category">Type</span></header><section><div><p>An identifier (usually a variable name) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L70-L72">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathLambda" href="#SBML.MathLambda"><code>SBML.MathLambda</code></a><span class="docstring-category">Type</span></header><section><div><p>Function definition (aka &quot;lambda&quot;) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L101-L103">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathTime" href="#SBML.MathTime"><code>SBML.MathTime</code></a><span class="docstring-category">Type</span></header><section><div><p>A special value representing the current time of the simulation, with a special name.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L85-L88">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.MathVal" href="#SBML.MathVal"><code>SBML.MathVal</code></a><span class="docstring-category">Type</span></header><section><div><p>A literal value (usually a numeric constant) in mathematical expression</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L63-L65">source</a></section></article><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>parameters</code>, <code>units</code>, <code>compartments</code>, <code>species</code> and <code>reactions</code> and <code>gene_products</code>, and additional <code>notes</code> and <code>annotation</code> (also present internally in some of the data fields). 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/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L184-L190">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>). Also may contains <code>notes</code> and <code>annotation</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L123-L128">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>, a <code>compartment</code> identifier, <code>formula</code>, <code>charge</code>, and additional <code>notes</code> and <code>annotation</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L143-L146">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="nohighlight">SBML.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>SBML.Model</code></a>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/structs.jl#L10-L22">source</a></section></article><h2 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></h2><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/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/version.jl#L2-L6">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.extractModel-Tuple{Ptr{Nothing}}" href="#SBML.extractModel-Tuple{Ptr{Nothing}}"><code>SBML.extractModel</code></a><span class="docstring-category">Method</span></header><section><div><p>&quot; function extractModel(mdl::VPtr)::SBML.Model</p><p>Take the <code>SBMLModel_t</code> pointer and extract all information required to make a valid <a href="#SBML.Model"><code>SBML.Model</code></a> structure.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L156-L162">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getAssociation-Tuple{Ptr{Nothing}}" href="#SBML.getAssociation-Tuple{Ptr{Nothing}}"><code>SBML.getAssociation</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getAssociation(x::VPtr)::GeneProductAssociation</code></pre><p>Convert a pointer to SBML <code>FbcAssociation_t</code> to the <code>GeneProductAssociation</code> tree structure.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L126-L131">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_bool-Tuple{Ptr{Nothing},Any,Any}" href="#SBML.get_optional_bool-Tuple{Ptr{Nothing},Any,Any}"><code>SBML.get_optional_bool</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_bool(x::VPtr, is_sym, get_sym)::Maybe{Bool}</code></pre><p>Helper for getting out boolean flags.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L38-L42">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_double-Tuple{Ptr{Nothing},Any,Any}" href="#SBML.get_optional_double-Tuple{Ptr{Nothing},Any,Any}"><code>SBML.get_optional_double</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}</code></pre><p>Helper for getting out C doubles aka Float64s.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L64-L68">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_int-Tuple{Ptr{Nothing},Any,Any}" href="#SBML.get_optional_int-Tuple{Ptr{Nothing},Any,Any}"><code>SBML.get_optional_int</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_int(x::VPtr, is_sym, get_sym)::Maybe{UInt}</code></pre><p>Helper for getting out unsigned integers.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L51-L55">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_string-Tuple{Ptr{Nothing},Any}" href="#SBML.get_optional_string-Tuple{Ptr{Nothing},Any}"><code>SBML.get_optional_string</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_string(x::VPtr, fn_sym)::Maybe{String}</code></pre><p>Like <a href="#SBML.get_string-Tuple{Ptr{Nothing},Any}"><code>get_string</code></a>, but returns <code>nothing</code> instead of throwing an exception.</p><p>This is used to get notes and annotations and several other things (see <code>get_notes</code>, <code>get_annotations</code>)</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L20-L28">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_string-Tuple{Ptr{Nothing},Any}" href="#SBML.get_string-Tuple{Ptr{Nothing},Any}"><code>SBML.get_string</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_string(x::VPtr, fn_sym)::Maybe{String}</code></pre><p>C-call the SBML function <code>fn_sym</code> with a single parameter <code>x</code>, interpret the result as a string and return it, or throw exception in case the pointer is NULL.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L4-L10">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.readSBML" href="#SBML.readSBML"><code>SBML.readSBML</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">function readSBML(fn::String, sbml_conversion = model-&gt;nothing)::SBML.Model</code></pre><p>Read the SBML from a XML file in <code>fn</code> and return the contained <code>SBML.Model</code>.</p><p>The <code>sbml_conversion</code> is a function that does an in-place modification of the single parameter, which is the C pointer to the loaded SBML document (C type <code>SBMLDocument*</code>). Several functions for doing that are prepared, including <a href="#SBML.set_level_and_version-Tuple{Any,Any}"><code>set_level_and_version</code></a>, <a href="#SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}"><code>libsbml_convert</code></a>, and <a href="#SBML.convert_simplify_math"><code>convert_simplify_math</code></a>.</p><p><strong>Example</strong></p><pre><code class="nohighlight">m = readSBML(&quot;my_model.xml&quot;, doc -&gt; begin
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>SBML.Model</code></a>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/structs.jl#L10-L22">source</a></section></article><h2 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></h2><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/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/version.jl#L2-L6">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.extractModel-Tuple{Ptr{Nothing}}" href="#SBML.extractModel-Tuple{Ptr{Nothing}}"><code>SBML.extractModel</code></a><span class="docstring-category">Method</span></header><section><div><p>&quot; function extractModel(mdl::VPtr)::SBML.Model</p><p>Take the <code>SBMLModel_t</code> pointer and extract all information required to make a valid <a href="#SBML.Model"><code>SBML.Model</code></a> structure.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L156-L162">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getAssociation-Tuple{Ptr{Nothing}}" href="#SBML.getAssociation-Tuple{Ptr{Nothing}}"><code>SBML.getAssociation</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getAssociation(x::VPtr)::GeneProductAssociation</code></pre><p>Convert a pointer to SBML <code>FbcAssociation_t</code> to the <code>GeneProductAssociation</code> tree structure.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L126-L131">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_bool-Tuple{Ptr{Nothing},Any,Any}" href="#SBML.get_optional_bool-Tuple{Ptr{Nothing},Any,Any}"><code>SBML.get_optional_bool</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_bool(x::VPtr, is_sym, get_sym)::Maybe{Bool}</code></pre><p>Helper for getting out boolean flags.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L38-L42">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_double-Tuple{Ptr{Nothing},Any,Any}" href="#SBML.get_optional_double-Tuple{Ptr{Nothing},Any,Any}"><code>SBML.get_optional_double</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_double(x::VPtr, is_sym, get_sym)::Maybe{Float64}</code></pre><p>Helper for getting out C doubles aka Float64s.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L64-L68">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_int-Tuple{Ptr{Nothing},Any,Any}" href="#SBML.get_optional_int-Tuple{Ptr{Nothing},Any,Any}"><code>SBML.get_optional_int</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_int(x::VPtr, is_sym, get_sym)::Maybe{UInt}</code></pre><p>Helper for getting out unsigned integers.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L51-L55">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_optional_string-Tuple{Ptr{Nothing},Any}" href="#SBML.get_optional_string-Tuple{Ptr{Nothing},Any}"><code>SBML.get_optional_string</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_optional_string(x::VPtr, fn_sym)::Maybe{String}</code></pre><p>Like <a href="#SBML.get_string-Tuple{Ptr{Nothing},Any}"><code>get_string</code></a>, but returns <code>nothing</code> instead of throwing an exception.</p><p>This is used to get notes and annotations and several other things (see <code>get_notes</code>, <code>get_annotations</code>)</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L20-L28">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.get_string-Tuple{Ptr{Nothing},Any}" href="#SBML.get_string-Tuple{Ptr{Nothing},Any}"><code>SBML.get_string</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">get_string(x::VPtr, fn_sym)::Maybe{String}</code></pre><p>C-call the SBML function <code>fn_sym</code> with a single parameter <code>x</code>, interpret the result as a string and return it, or throw exception in case the pointer is NULL.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L4-L10">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.readSBML" href="#SBML.readSBML"><code>SBML.readSBML</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">function readSBML(fn::String, sbml_conversion = model-&gt;nothing)::SBML.Model</code></pre><p>Read the SBML from a XML file in <code>fn</code> and return the contained <code>SBML.Model</code>.</p><p>The <code>sbml_conversion</code> is a function that does an in-place modification of the single parameter, which is the C pointer to the loaded SBML document (C type <code>SBMLDocument*</code>). Several functions for doing that are prepared, including <a href="#SBML.set_level_and_version-Tuple{Any,Any}"><code>set_level_and_version</code></a>, <a href="#SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}"><code>libsbml_convert</code></a>, and <a href="#SBML.convert_simplify_math"><code>convert_simplify_math</code></a>.</p><p><strong>Example</strong></p><pre><code class="nohighlight">m = readSBML(&quot;my_model.xml&quot;, doc -&gt; begin
set_level_and_version(3, 1)(doc)
convert_simplify_math(doc)
end)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/readsbml.jl#L77-L95">source</a></section></article><h2 id="libsbml-representation-converters"><a class="docs-heading-anchor" href="#libsbml-representation-converters"><code>libsbml</code> representation converters</a><a id="libsbml-representation-converters-1"></a><a class="docs-heading-anchor-permalink" href="#libsbml-representation-converters" title="Permalink"></a></h2><p>The converters are intended to be used as parameters of <a href="#SBML.readSBML"><code>readSBML</code></a>.</p><article class="docstring"><header><a class="docstring-binding" id="SBML.convert_simplify_math" href="#SBML.convert_simplify_math"><code>SBML.convert_simplify_math</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">convert_simplify_math</code></pre><p>Shortcut for <a href="#SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}"><code>libsbml_convert</code></a> that expands functions, local parameters, and initial assignments in the SBML document.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/converters.jl#L64-L69">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}" href="#SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}"><code>SBML.libsbml_convert</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">libsbml_convert(conversion_options::Vector{Pair{String, Dict{String, String}}})</code></pre><p>A converter that runs the SBML conversion routine, with specified conversion options. The argument is a vector of pairs to allow specifying the order of conversions.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/converters.jl#L20-L26">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.libsbml_convert-Tuple{String}" href="#SBML.libsbml_convert-Tuple{String}"><code>SBML.libsbml_convert</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">libsbml_convert(converter::String; kwargs...)</code></pre><p>Quickly construct a single run of a <code>libsbml</code> converter from keyword arguments.</p><p><strong>Example</strong></p><pre><code class="nohighlight">readSBML(&quot;example.xml&quot;, libsbml_convert(&quot;stripPackage&quot;, package=&quot;layout&quot;))</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/converters.jl#L50-L59">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.set_level_and_version-Tuple{Any,Any}" href="#SBML.set_level_and_version-Tuple{Any,Any}"><code>SBML.set_level_and_version</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">set_level_and_version(level, version)</code></pre><p>A converter to pass into <a href="#SBML.readSBML"><code>readSBML</code></a> that enforces certain SBML level and version.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/converters.jl#L2-L7">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{SBML.Model}" href="#SBML.getLBs-Tuple{SBML.Model}"><code>SBML.getLBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getLBs(m::SBML.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/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/utils.jl#L27-L33">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getOCs-Tuple{SBML.Model}" href="#SBML.getOCs-Tuple{SBML.Model}"><code>SBML.getOCs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getOCs(m::SBML.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/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/utils.jl#L47-L51">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getS-Tuple{SBML.Model}" href="#SBML.getS-Tuple{SBML.Model}"><code>SBML.getS</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getS(m::SBML.Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{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>SBML.Model</code>. Returns a tuple with these values.</p><p>The matrix is sparse by default (initially constructed by <code>SparseArrays.spzeros</code>). You can fill in a custom empty matrix constructed to argument <code>zeros</code>; e.g. running with <code>zeros=zeros</code> will produce a dense matrix.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/utils.jl#L1-L11">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getUBs-Tuple{SBML.Model}" href="#SBML.getUBs-Tuple{SBML.Model}"><code>SBML.getUBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getUBs(m::SBML.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/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/utils.jl#L38-L42">source</a></section></article><h2 id="Math-and-Symbolics.jl-compatibility"><a class="docs-heading-anchor" href="#Math-and-Symbolics.jl-compatibility">Math and <code>Symbolics.jl</code> compatibility</a><a id="Math-and-Symbolics.jl-compatibility-1"></a><a class="docs-heading-anchor-permalink" href="#Math-and-Symbolics.jl-compatibility" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="SBML.default_symbolics_mapping" href="#SBML.default_symbolics_mapping"><code>SBML.default_symbolics_mapping</code></a><span class="docstring-category">Constant</span></header><section><div><pre><code class="language-julia">default_symbolics_mapping :: Dict{String,Any}</code></pre><p>Default mapping of SBML function names to Julia functions, represented as a dictionary from Strings (SBML names) to anything <code>eval</code>uable as Julia&amp;Symbolics functions, such as symbols and expressions.</p><p>The default mapping only contains the basic SBML functions that are unambiguously represented in Julia; it is supposed to be extended by the user if more functions need to be supported.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/symbolics.jl#L2-L12">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Base.convert-Tuple{Type{Symbolics.Num},SBML.Math}" href="#Base.convert-Tuple{Type{Symbolics.Num},SBML.Math}"><code>Base.convert</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">Base.convert(
end)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/readsbml.jl#L77-L95">source</a></section></article><h2 id="libsbml-representation-converters"><a class="docs-heading-anchor" href="#libsbml-representation-converters"><code>libsbml</code> representation converters</a><a id="libsbml-representation-converters-1"></a><a class="docs-heading-anchor-permalink" href="#libsbml-representation-converters" title="Permalink"></a></h2><p>The converters are intended to be used as parameters of <a href="#SBML.readSBML"><code>readSBML</code></a>.</p><article class="docstring"><header><a class="docstring-binding" id="SBML.convert_simplify_math" href="#SBML.convert_simplify_math"><code>SBML.convert_simplify_math</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">convert_simplify_math</code></pre><p>Shortcut for <a href="#SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}"><code>libsbml_convert</code></a> that expands functions, local parameters, and initial assignments in the SBML document.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/converters.jl#L64-L69">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}" href="#SBML.libsbml_convert-Tuple{AbstractArray{var&quot;#s50&quot;,1} where var&quot;#s50&quot;&lt;:(Pair{String,var&quot;#s49&quot;} where var&quot;#s49&quot;&lt;:AbstractDict{String,String})}"><code>SBML.libsbml_convert</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">libsbml_convert(conversion_options::Vector{Pair{String, Dict{String, String}}})</code></pre><p>A converter that runs the SBML conversion routine, with specified conversion options. The argument is a vector of pairs to allow specifying the order of conversions.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/converters.jl#L20-L26">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.libsbml_convert-Tuple{String}" href="#SBML.libsbml_convert-Tuple{String}"><code>SBML.libsbml_convert</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">libsbml_convert(converter::String; kwargs...)</code></pre><p>Quickly construct a single run of a <code>libsbml</code> converter from keyword arguments.</p><p><strong>Example</strong></p><pre><code class="nohighlight">readSBML(&quot;example.xml&quot;, libsbml_convert(&quot;stripPackage&quot;, package=&quot;layout&quot;))</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/converters.jl#L50-L59">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.set_level_and_version-Tuple{Any,Any}" href="#SBML.set_level_and_version-Tuple{Any,Any}"><code>SBML.set_level_and_version</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">set_level_and_version(level, version)</code></pre><p>A converter to pass into <a href="#SBML.readSBML"><code>readSBML</code></a> that enforces certain SBML level and version.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/converters.jl#L2-L7">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{SBML.Model}" href="#SBML.getLBs-Tuple{SBML.Model}"><code>SBML.getLBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getLBs(m::SBML.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/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/utils.jl#L27-L33">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getOCs-Tuple{SBML.Model}" href="#SBML.getOCs-Tuple{SBML.Model}"><code>SBML.getOCs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getOCs(m::SBML.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/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/utils.jl#L47-L51">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getS-Tuple{SBML.Model}" href="#SBML.getS-Tuple{SBML.Model}"><code>SBML.getS</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getS(m::SBML.Model; zeros=spzeros)::Tuple{Vector{String},Vector{String},AbstractMatrix{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>SBML.Model</code>. Returns a tuple with these values.</p><p>The matrix is sparse by default (initially constructed by <code>SparseArrays.spzeros</code>). You can fill in a custom empty matrix constructed to argument <code>zeros</code>; e.g. running with <code>zeros=zeros</code> will produce a dense matrix.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/utils.jl#L1-L11">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.getUBs-Tuple{SBML.Model}" href="#SBML.getUBs-Tuple{SBML.Model}"><code>SBML.getUBs</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">function getUBs(m::SBML.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/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/utils.jl#L38-L42">source</a></section></article><h2 id="Math-and-Symbolics.jl-compatibility"><a class="docs-heading-anchor" href="#Math-and-Symbolics.jl-compatibility">Math and <code>Symbolics.jl</code> compatibility</a><a id="Math-and-Symbolics.jl-compatibility-1"></a><a class="docs-heading-anchor-permalink" href="#Math-and-Symbolics.jl-compatibility" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="SBML.default_symbolics_mapping" href="#SBML.default_symbolics_mapping"><code>SBML.default_symbolics_mapping</code></a><span class="docstring-category">Constant</span></header><section><div><pre><code class="language-julia">default_symbolics_mapping :: Dict{String,Any}</code></pre><p>Default mapping of SBML function names to Julia functions, represented as a dictionary from Strings (SBML names) to anything <code>eval</code>uable as Julia&amp;Symbolics functions, such as symbols and expressions.</p><p>The default mapping only contains the basic SBML functions that are unambiguously represented in Julia; it is supposed to be extended by the user if more functions need to be supported.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/symbolics.jl#L2-L12">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Base.convert-Tuple{Type{Symbolics.Num},SBML.Math}" href="#Base.convert-Tuple{Type{Symbolics.Num},SBML.Math}"><code>Base.convert</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">Base.convert(
::Type{Num},
x::SBML.Math;
mapping = default_symbolics_mapping,
convert_time = (x::SBML.MathTime) -&gt; Num(Variable(Symbol(x.id))).val,
)</code></pre><p>Convert SBML.<a href="#SBML.Math"><code>Math</code></a> to <code>Num</code> type from Symbolics package. The conversion of functions can be customized by supplying a custom mapping; if nothing is supplied, <a href="#SBML.default_symbolics_mapping"><code>default_symbolics_mapping</code></a> that translates basic functions to their Julia equivalents is assumed.</p><p>Translation of <a href="#SBML.MathLambda"><code>MathLambda</code></a> is not supported by Symbolics.</p><p><a href="#SBML.MathTime"><code>MathTime</code></a> is handled specially, the function from the argument <code>convert_time</code> is called to possibly specify any desired behavior. By default, it just creates a variable with the same name as the time variable name stored in SBML.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/symbolics.jl#L32-L51">source</a></section></article><h3 id="Internal-math-helpers"><a class="docs-heading-anchor" href="#Internal-math-helpers">Internal math helpers</a><a id="Internal-math-helpers-1"></a><a class="docs-heading-anchor-permalink" href="#Internal-math-helpers" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="SBML.ast_is-Tuple{Ptr{Nothing},Symbol}" href="#SBML.ast_is-Tuple{Ptr{Nothing},Symbol}"><code>SBML.ast_is</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">ast_is(ast::VPtr, what::Symbol)::Bool</code></pre><p>Helper for quickly recognizing kinds of ASTs</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/math.jl#L2-L6">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.parse_math-Tuple{Ptr{Nothing}}" href="#SBML.parse_math-Tuple{Ptr{Nothing}}"><code>SBML.parse_math</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">parse_math(ast::VPtr)::Math</code></pre><p>This attempts to parse out a decent Julia-esque (<a href="#SBML.Math"><code>Math</code></a> AST from a pointer to <code>ASTNode_t</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/math.jl#L19-L24">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.parse_math_children-Tuple{Ptr{Nothing}}" href="#SBML.parse_math_children-Tuple{Ptr{Nothing}}"><code>SBML.parse_math_children</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">parse_math_children(ast::VPtr)::Vector{Math}</code></pre><p>Recursively parse all children of an AST node.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/74e86ecfdcd441d11a8b0c1ca1e4f4a67de2e4a1/src/math.jl#L9-L13">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="Tuesday 22 June 2021 08:18">Tuesday 22 June 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
)</code></pre><p>Convert SBML.<a href="#SBML.Math"><code>Math</code></a> to <code>Num</code> type from Symbolics package. The conversion of functions can be customized by supplying a custom mapping; if nothing is supplied, <a href="#SBML.default_symbolics_mapping"><code>default_symbolics_mapping</code></a> that translates basic functions to their Julia equivalents is assumed.</p><p>Translation of <a href="#SBML.MathLambda"><code>MathLambda</code></a> is not supported by Symbolics.</p><p><a href="#SBML.MathTime"><code>MathTime</code></a> is handled specially, the function from the argument <code>convert_time</code> is called to possibly specify any desired behavior. By default, it just creates a variable with the same name as the time variable name stored in SBML.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/symbolics.jl#L32-L51">source</a></section></article><h3 id="Internal-math-helpers"><a class="docs-heading-anchor" href="#Internal-math-helpers">Internal math helpers</a><a id="Internal-math-helpers-1"></a><a class="docs-heading-anchor-permalink" href="#Internal-math-helpers" title="Permalink"></a></h3><article class="docstring"><header><a class="docstring-binding" id="SBML.ast_is-Tuple{Ptr{Nothing},Symbol}" href="#SBML.ast_is-Tuple{Ptr{Nothing},Symbol}"><code>SBML.ast_is</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">ast_is(ast::VPtr, what::Symbol)::Bool</code></pre><p>Helper for quickly recognizing kinds of ASTs</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/math.jl#L2-L6">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.parse_math-Tuple{Ptr{Nothing}}" href="#SBML.parse_math-Tuple{Ptr{Nothing}}"><code>SBML.parse_math</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">parse_math(ast::VPtr)::Math</code></pre><p>This attempts to parse out a decent Julia-esque (<a href="#SBML.Math"><code>Math</code></a> AST from a pointer to <code>ASTNode_t</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/math.jl#L19-L24">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="SBML.parse_math_children-Tuple{Ptr{Nothing}}" href="#SBML.parse_math_children-Tuple{Ptr{Nothing}}"><code>SBML.parse_math_children</code></a><span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">parse_math_children(ast::VPtr)::Vector{Math}</code></pre><p>Recursively parse all children of an AST node.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/LCSB-BioCore/SBML.jl/blob/41a25d0d9ae65f6b2e2af1299065b720961fd588/src/math.jl#L9-L13">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="Tuesday 22 June 2021 08:21">Tuesday 22 June 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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