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‎julia-docs/dev/docstrings/medyan.addreaction--da9bd35e7d1df7c3.html‎

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<ul>
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<li><a href="#medyan.addreaction" id="toc-medyan.addreaction" class="nav-link active" data-scroll-target="#medyan.addreaction"><code>MEDYAN.addreaction!</code></a>
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<li><a href="#tuple-medyan.sysdef--medyan.compartmentreaction--028b8b53a1777d4b" id="toc-tuple-medyan.sysdef--medyan.compartmentreaction--028b8b53a1777d4b" class="nav-link" data-scroll-target="#tuple-medyan.sysdef--medyan.compartmentreaction--028b8b53a1777d4b"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, MEDYAN.CompartmentReaction}</code></a></li>
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<li><a href="#tuple-medyan.sysdef--abstractstring--float64--int64--458efa379d290938" id="toc-tuple-medyan.sysdef--abstractstring--float64--int64--458efa379d290938" class="nav-link" data-scroll-target="#tuple-medyan.sysdef--abstractstring--float64--int64--458efa379d290938"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, AbstractString, Float64, Int64}</code></a></li>
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<section id="medyan.addreaction" class="level1">
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<h1><code>MEDYAN.addreaction!</code></h1>
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<section id="tuple-medyan.sysdef--medyan.compartmentreaction--028b8b53a1777d4b" class="level2">
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<h2 class="anchored" data-anchor-id="tuple-medyan.sysdef--medyan.compartmentreaction--028b8b53a1777d4b"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, MEDYAN.CompartmentReaction}</code></h2>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">addreaction!</span>(s<span class="op">::</span><span class="dt">SysDef</span>,reaction<span class="op">::</span><span class="dt">CompartmentReaction</span>)<span class="op">::</span><span class="dt">SysDef</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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</section>
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<section id="tuple-medyan.sysdef--abstractstring--float64--int64--458efa379d290938" class="level2">
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<h2 class="anchored" data-anchor-id="tuple-medyan.sysdef--abstractstring--float64--int64--458efa379d290938"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, AbstractString, Float64, Int64}</code></h2>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb2"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">addreaction!</span>(s<span class="op">::</span><span class="dt">SysDef</span>,reactionexpr<span class="op">::</span><span class="dt">AbstractString</span>,rate<span class="op">::</span><span class="dt">Float64</span>,invvolumepower<span class="op">::</span><span class="dt">Int</span>)<span class="op">::</span><span class="dt">SysDef</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">addreaction!</span>(s<span class="op">::</span><span class="dt">SysDef</span>,reactionexpr<span class="op">::</span><span class="dt">AbstractString</span>,rate<span class="op">::</span><span class="dt">Float64</span>,invvolumepower<span class="op">::</span><span class="dt">Int</span>)<span class="op">::</span><span class="dt">SysDef</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Add a reaction to the system. Return s</p>
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<p><code>reactionexpr</code> is a string describing the reaction stoichiometry</p>
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<p><code>reactionexpr</code> is comprised of reactant and product parts seperated by a <code>"--&gt;"</code></p>
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<section id="example-good-reactionexpr" class="level1">
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<h1>Example good <code>reactionexpr</code></h1>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb3"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a + diffusing.b --&gt; diffusing.c"</span></span>
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<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.c --&gt; diffusing.a + diffusing.b"</span></span>
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<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="st">"+ + diffusing.c + --&gt; + diffusing.a + + diffusing.b + +"</span></span>
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<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="st">" --&gt; diffusing.a + diffusing.b"</span></span>
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<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a + diffusing.b --&gt; "</span></span>
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<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a + diffusing.a --&gt; "</span></span>
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<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a><span class="st">"2diffusing.a --&gt; "</span></span>
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<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a><span class="st">"2diffusing.a --&gt; 20diffusing.a"</span></span>
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<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.c + diffusing.b --&gt; diffusing.c + diffusing.b"</span></span>
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<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.rate1b --&gt; fixedspecies.g"</span></span>
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<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.rate1b + fixedspecies.g --&gt; fixedspecies.g"</span></span>
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<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.rate1b + 23fixedspecies.g --&gt; fixedspecies.g"</span></span>
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<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.g --&gt; fixedspecies.rate1b + 23fixedspecies.g"</span></span>
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<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.g + fixedspecies.rate1b--&gt; 2fixedspecies.rate1b + 23fixedspecies.g"</span></span>
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<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a><span class="st">"filamentsite.MT.d --&gt; filamentsite.MT.d"</span></span>
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<span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a><span class="st">"filamentsite.MT.d + diffusing.a --&gt; filamentsite.MT.d"</span></span>
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<span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.g --&gt; diffusing.a"</span></span>
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<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a --&gt; fixedspecies.g"</span></span>
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<span id="cb3-19"><a href="#cb3-19" aria-hidden="true" tabindex="-1"></a><span class="st">"filamentsite.actin.pm + diffusing.a --&gt; filamentsite.actin.pm"</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb2"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a + diffusing.b --&gt; diffusing.c"</span></span>
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<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.c --&gt; diffusing.a + diffusing.b"</span></span>
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<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="st">"+ + diffusing.c + --&gt; + diffusing.a + + diffusing.b + +"</span></span>
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<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="st">" --&gt; diffusing.a + diffusing.b"</span></span>
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<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a + diffusing.b --&gt; "</span></span>
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<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a + diffusing.a --&gt; "</span></span>
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<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a><span class="st">"2diffusing.a --&gt; "</span></span>
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<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a><span class="st">"2diffusing.a --&gt; 20diffusing.a"</span></span>
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<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.c + diffusing.b --&gt; diffusing.c + diffusing.b"</span></span>
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<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.rate1b --&gt; fixedspecies.g"</span></span>
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<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.rate1b + fixedspecies.g --&gt; fixedspecies.g"</span></span>
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<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.rate1b + 23fixedspecies.g --&gt; fixedspecies.g"</span></span>
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<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.g --&gt; fixedspecies.rate1b + 23fixedspecies.g"</span></span>
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<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.g + fixedspecies.rate1b--&gt; 2fixedspecies.rate1b + 23fixedspecies.g"</span></span>
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<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a><span class="st">"filamentsite.MT.d --&gt; filamentsite.MT.d"</span></span>
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<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a><span class="st">"filamentsite.MT.d + diffusing.a --&gt; filamentsite.MT.d"</span></span>
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<span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a><span class="st">"fixedspecies.g --&gt; diffusing.a"</span></span>
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<span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a><span class="st">"diffusing.a --&gt; fixedspecies.g"</span></span>
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<span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a><span class="st">"filamentsite.actin.pm + diffusing.a --&gt; filamentsite.actin.pm"</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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‎julia-docs/dev/docstrings/medyan.addreactioncallback--9c9d46adeded2d88.html‎

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<ul>
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<li><a href="#medyan.addreactioncallback" id="toc-medyan.addreactioncallback" class="nav-link active" data-scroll-target="#medyan.addreactioncallback"><code>MEDYAN.addreactioncallback!</code></a>
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<li><a href="#tuple-medyan.sysdef--medyan.compartmentreaction--any--36763138c31ba7fa" id="toc-tuple-medyan.sysdef--medyan.compartmentreaction--any--36763138c31ba7fa" class="nav-link" data-scroll-target="#tuple-medyan.sysdef--medyan.compartmentreaction--any--36763138c31ba7fa"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, MEDYAN.CompartmentReaction, Any}</code></a></li>
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<li><a href="#tuple-medyan.sysdef--medyan.bulkreaction--any--bad9b85c7303199e" id="toc-tuple-medyan.sysdef--medyan.bulkreaction--any--bad9b85c7303199e" class="nav-link" data-scroll-target="#tuple-medyan.sysdef--medyan.bulkreaction--any--bad9b85c7303199e"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, MEDYAN.BulkReaction, Any}</code></a></li>
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<li><a href="#tuple-medyan.sysdef--abstractstring--float64--int64--any--ecdb462076761cce" id="toc-tuple-medyan.sysdef--abstractstring--float64--int64--any--ecdb462076761cce" class="nav-link" data-scroll-target="#tuple-medyan.sysdef--abstractstring--float64--int64--any--ecdb462076761cce"><code data-shortcodes="false">Tuple{MEDYAN.SysDef, AbstractString, Float64, Int64, Any}</code></a></li>
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<div class="toc-actions"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.addreactioncallback--9c9d46adeded2d88.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/medyan-dev/MEDYAN.jl/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
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<section id="medyan.addreactioncallback" class="level1">
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<h1><code>MEDYAN.addreactioncallback!</code></h1>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">addreactioncallback!</span>(s<span class="op">::</span><span class="dt">SysDef</span>, reactantexpr<span class="op">::</span><span class="dt">AbstractString</span>, rate<span class="op">::</span><span class="dt">Float64</span>, invvolumepower<span class="op">::</span><span class="dt">Int</span>, callback)<span class="op">::</span><span class="dt">SysDef</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Like <a href="../docstrings/medyan.addreaction--da9bd35e7d1df7c3.html"><code>addreaction!</code></a> but also adds <code>callback</code>. <code>callback</code> is called when the reaction happens with input of <code>MEDYAN.Context</code> and <code>Int</code> the compartment id where the reaction happened.</p>
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<p>The reaction should normally have no net stoichiometry because the callback should handle updating species counts. If an <code>AbstractString</code> is passed instead of a <code>CompartmentReaction</code> for the reaction, that string will be parsed to determine the reactants. The net stoichiometry will be zero.</p>
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<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb1"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">addreactioncallback!</span>(s<span class="op">::</span><span class="dt">SysDef</span>, reactantexpr<span class="op">::</span><span class="dt">AbstractString</span>, rate<span class="op">::</span><span class="dt">Float64</span>, invvolumepower<span class="op">::</span><span class="dt">Int</span>, callback)<span class="op">::</span><span class="dt">SysDef</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
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<p>Like <a href="../docstrings/medyan.addreaction--da9bd35e7d1df7c3.html"><code>addreaction!</code></a> but also adds <code>callback</code>. <code>callback</code> is called when the reaction happens with input of <code>MEDYAN.Context</code> and <code>Int</code> the chem_voxel id where the reaction happened.</p>
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<p>The callback should handle updating species counts.</p>
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<p><code>MEDYAN.errorcheck_addcallback(callback,s::SysDef)</code> can optionally be overloaded to add errorchecking when the callback is added.</p>
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<p>Callback for bulk reactions: Context -&gt; Nothing.</p>
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