Skip to content

Commit 5f30e83

Browse files
author
Documenter.jl
committed
build based on f4d8736
1 parent dfe8924 commit 5f30e83

14 files changed

Lines changed: 2046 additions & 2046 deletions

‎julia-docs/dev/docstrings.html‎

Lines changed: 179 additions & 179 deletions
Large diffs are not rendered by default.

‎julia-docs/dev/docstrings/medyan.add_filament_params--74c7d0081157ca31.html‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -210,7 +210,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.sysdef--symbol--any--444c61f2a
210210
<div class="callout-body-container">
211211
<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">add_filament_params!</span>(s<span class="op">::</span><span class="dt">SysDef</span>, filament_name<span class="op">::</span><span class="dt">Symbol</span>, filament_params<span class="op">::</span><span class="dt">FilamentMechParams</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
212212
<p>Update the filament mechanical parameters for an existing filament type.</p>
213-
<p>The filament type must already exist in <code>s.filament</code> (typically added via <a href="../docstrings/medyan.add_fila_type--006e34b8bafba683.html"><code>add_fila_type!</code></a>.</p>
213+
<p>The filament type must already exist in <code>s.filament</code> (typically added via <a href="../docstrings/medyan.def_fila_type--5a1f6234215ea82d.html"><code>def_fila_type!</code></a>.</p>
214214
<section id="arguments" class="level1">
215215
<h1>Arguments</h1>
216216
<ul>
@@ -222,7 +222,7 @@ <h1>Arguments</h1>
222222
<section id="returns" class="level1">
223223
<h1>Returns</h1>
224224
<p>The modified <code>SysDef</code>.</p>
225-
<p>See also: <a href="../docstrings/medyan.add_fila_type--006e34b8bafba683.html"><code>add_fila_type!</code></a> to add a new filament type with its parameters in one step.</p>
225+
<p>See also: <a href="../docstrings/medyan.def_fila_type--5a1f6234215ea82d.html"><code>def_fila_type!</code></a> to add a new filament type with its parameters in one step.</p>
226226
</section>
227227
</div>
228228
</div>

‎julia-docs/dev/docstrings/medyan.def_fila_reaction--070b0fa01eaea608.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -258,7 +258,7 @@ <h3 class="anchored" data-anchor-id="geometry">Geometry</h3>
258258
<h1>Examples</h1>
259259
<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="im">using</span> <span class="bu">MEDYAN</span></span>
260260
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>s <span class="op">=</span> MEDYAN.<span class="fu">SysDef</span>()</span>
261-
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">add_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>b, <span class="op">:</span>c], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
261+
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>b, <span class="op">:</span>c], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
262262
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a></span>
263263
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="co"># Aging: every :a monomer transitions to :b</span></span>
264264
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_reaction!</span>(s;</span>

‎julia-docs/dev/docstrings/medyan.def_fila_tip_reaction--488aa3a14ff39688.html‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -252,7 +252,7 @@ <h3 class="anchored" data-anchor-id="rate">Rate</h3>
252252
<h1>Examples</h1>
253253
<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="im">using</span> <span class="bu">MEDYAN</span></span>
254254
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>s <span class="op">=</span> MEDYAN.<span class="fu">SysDef</span>()</span>
255-
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">add_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>plusend, <span class="op">:</span>minusend], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
255+
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>plusend, <span class="op">:</span>minusend], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
256256
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="fu">def_diffusing_species!</span>(s, <span class="op">:</span>actin_mon; coeff<span class="op">=</span><span class="fl">2.5e7</span>)</span>
257257
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a></span>
258258
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Plus-end polymerization: add one monomer (bimolecular with diffusing actin)</span></span>

julia-docs/dev/docstrings/medyan.add_fila_type--006e34b8bafba683.html renamed to julia-docs/dev/docstrings/medyan.def_fila_type--5a1f6234215ea82d.html

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
88

99

10-
<title>medyan.add_fila_type--006e34b8bafba683 – MEDYAN.jl</title>
10+
<title>medyan.def_fila_type--5a1f6234215ea82d – MEDYAN.jl</title>
1111
<style>
1212
code{white-space: pre-wrap;}
1313
span.smallcaps{font-variant: small-caps;}
@@ -185,21 +185,21 @@
185185
<h2 id="toc-title">On this page</h2>
186186

187187
<ul>
188-
<li><a href="#medyan.add_fila_type" id="toc-medyan.add_fila_type" class="nav-link active" data-scroll-target="#medyan.add_fila_type"><code>MEDYAN.add_fila_type!</code></a>
188+
<li><a href="#medyan.def_fila_type" id="toc-medyan.def_fila_type" class="nav-link active" data-scroll-target="#medyan.def_fila_type"><code>MEDYAN.def_fila_type!</code></a>
189189
<ul class="collapse">
190190
<li><a href="#tuple-medyan.sysdef--efaa49a98644904f" id="toc-tuple-medyan.sysdef--efaa49a98644904f" class="nav-link" data-scroll-target="#tuple-medyan.sysdef--efaa49a98644904f"><code data-shortcodes="false">Tuple{MEDYAN.SysDef}</code></a></li>
191191
</ul></li>
192192
</ul>
193-
<div class="toc-actions"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.add_fila_type--006e34b8bafba683.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>
193+
<div class="toc-actions"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.def_fila_type--5a1f6234215ea82d.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>
194194
</div>
195195
<!-- main -->
196196
<main class="content" id="quarto-document-content"><header id="title-block-header" class="quarto-title-block"></header>
197197

198198

199199

200200

201-
<section id="medyan.add_fila_type" class="level1">
202-
<h1><code>MEDYAN.add_fila_type!</code></h1>
201+
<section id="medyan.def_fila_type" class="level1">
202+
<h1><code>MEDYAN.def_fila_type!</code></h1>
203203
<section id="tuple-medyan.sysdef--efaa49a98644904f" class="level2">
204204
<h2 class="anchored" data-anchor-id="tuple-medyan.sysdef--efaa49a98644904f"><code data-shortcodes="false">Tuple{MEDYAN.SysDef}</code></h2>
205205
<div class="callout callout-style-simple callout-note no-icon">
@@ -208,7 +208,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.sysdef--efaa49a98644904f"><cod
208208
<i class="callout-icon no-icon"></i>
209209
</div>
210210
<div class="callout-body-container">
211-
<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">add_fila_type!</span>(s<span class="op">::</span><span class="dt">SysDef</span>; name<span class="op">::</span><span class="dt">Symbol</span>, mono_states<span class="op">::</span><span class="dt">Vector{Symbol}</span>, param<span class="op">::</span><span class="dt">FilamentMechParams</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
211+
<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">def_fila_type!</span>(s<span class="op">::</span><span class="dt">SysDef</span>; name<span class="op">::</span><span class="dt">Symbol</span>, mono_states<span class="op">::</span><span class="dt">Vector{Symbol}</span>, param<span class="op">::</span><span class="dt">FilamentMechParams</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
212212
<p>Add a new filament type to the system definition.</p>
213213
<section id="arguments" class="level1">
214214
<h1>Arguments</h1>
@@ -644,4 +644,4 @@ <h1>Throws</h1>
644644

645645

646646

647-
<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.add_fila_type--006e34b8bafba683.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></div></div></footer></body></html>
647+
<footer class="footer"><div class="nav-footer"><div class="nav-footer-center"><div class="toc-actions d-sm-block d-md-none"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.def_fila_type--5a1f6234215ea82d.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></div></div></footer></body></html>

‎julia-docs/dev/docstrings/src/sys_def.html‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -190,7 +190,7 @@ <h2 id="toc-title">On this page</h2>
190190
<li><a href="#medyan.add_diffusion_coeff--a77d1ef833cfdedd" id="toc-medyan.add_diffusion_coeff--a77d1ef833cfdedd" class="nav-link" data-scroll-target="#medyan.add_diffusion_coeff--a77d1ef833cfdedd"><code>MEDYAN.add_diffusion_coeff!</code></a></li>
191191
<li><a href="#medyan.def_diffusing_species--e07d4f4fa5062c57" id="toc-medyan.def_diffusing_species--e07d4f4fa5062c57" class="nav-link" data-scroll-target="#medyan.def_diffusing_species--e07d4f4fa5062c57"><code>MEDYAN.def_diffusing_species!</code></a></li>
192192
<li><a href="#medyan.def_fixed_species--490fb150d53e2870" id="toc-medyan.def_fixed_species--490fb150d53e2870" class="nav-link" data-scroll-target="#medyan.def_fixed_species--490fb150d53e2870"><code>MEDYAN.def_fixed_species!</code></a></li>
193-
<li><a href="#medyan.add_fila_type--006e34b8bafba683" id="toc-medyan.add_fila_type--006e34b8bafba683" class="nav-link" data-scroll-target="#medyan.add_fila_type--006e34b8bafba683"><code>MEDYAN.add_fila_type!</code></a></li>
193+
<li><a href="#medyan.def_fila_type--5a1f6234215ea82d" id="toc-medyan.def_fila_type--5a1f6234215ea82d" class="nav-link" data-scroll-target="#medyan.def_fila_type--5a1f6234215ea82d"><code>MEDYAN.def_fila_type!</code></a></li>
194194
<li><a href="#medyan.add_filament_params--74c7d0081157ca31" id="toc-medyan.add_filament_params--74c7d0081157ca31" class="nav-link" data-scroll-target="#medyan.add_filament_params--74c7d0081157ca31"><code>MEDYAN.add_filament_params!</code></a></li>
195195
<li><a href="#medyan.addfilamentsite--eb6bfd871a21b6f4" id="toc-medyan.addfilamentsite--eb6bfd871a21b6f4" class="nav-link" data-scroll-target="#medyan.addfilamentsite--eb6bfd871a21b6f4"><code>MEDYAN.addfilamentsite!</code></a></li>
196196
<li><a href="#medyan.addfilamentendsite--95612d72d1fda05f" id="toc-medyan.addfilamentendsite--95612d72d1fda05f" class="nav-link" data-scroll-target="#medyan.addfilamentendsite--95612d72d1fda05f"><code>MEDYAN.addfilamentendsite!</code></a></li>
@@ -309,15 +309,15 @@ <h1>Throws</h1>
309309
</div>
310310
</div>
311311
</section>
312-
<section id="medyan.add_fila_type--006e34b8bafba683" class="level2">
313-
<h2 class="anchored" data-anchor-id="medyan.add_fila_type--006e34b8bafba683"><a href="../../docstrings/medyan.add_fila_type--006e34b8bafba683.html"><code>MEDYAN.add_fila_type!</code></a></h2>
312+
<section id="medyan.def_fila_type--5a1f6234215ea82d" class="level2">
313+
<h2 class="anchored" data-anchor-id="medyan.def_fila_type--5a1f6234215ea82d"><a href="../../docstrings/medyan.def_fila_type--5a1f6234215ea82d.html"><code>MEDYAN.def_fila_type!</code></a></h2>
314314
<div class="callout callout-style-simple callout-note no-icon">
315315
<div class="callout-body d-flex">
316316
<div class="callout-icon-container">
317317
<i class="callout-icon no-icon"></i>
318318
</div>
319319
<div class="callout-body-container">
320-
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb4"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">add_fila_type!</span>(s<span class="op">::</span><span class="dt">SysDef</span>; name<span class="op">::</span><span class="dt">Symbol</span>, mono_states<span class="op">::</span><span class="dt">Vector{Symbol}</span>, param<span class="op">::</span><span class="dt">FilamentMechParams</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
320+
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb4"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_type!</span>(s<span class="op">::</span><span class="dt">SysDef</span>; name<span class="op">::</span><span class="dt">Symbol</span>, mono_states<span class="op">::</span><span class="dt">Vector{Symbol}</span>, param<span class="op">::</span><span class="dt">FilamentMechParams</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
321321
<p>Add a new filament type to the system definition.</p>
322322
<section id="arguments-3" class="level1">
323323
<h1>Arguments</h1>
@@ -353,7 +353,7 @@ <h2 class="anchored" data-anchor-id="medyan.add_filament_params--74c7d0081157ca3
353353
<div class="callout-body-container">
354354
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb5"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">add_filament_params!</span>(s<span class="op">::</span><span class="dt">SysDef</span>, filament_name<span class="op">::</span><span class="dt">Symbol</span>, filament_params<span class="op">::</span><span class="dt">FilamentMechParams</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
355355
<p>Update the filament mechanical parameters for an existing filament type.</p>
356-
<p>The filament type must already exist in <code>s.filament</code> (typically added via <a href="../../docstrings/medyan.add_fila_type--006e34b8bafba683.html"><code>add_fila_type!</code></a>.</p>
356+
<p>The filament type must already exist in <code>s.filament</code> (typically added via <a href="../../docstrings/medyan.def_fila_type--5a1f6234215ea82d.html"><code>def_fila_type!</code></a>.</p>
357357
<section id="arguments-4" class="level1">
358358
<h1>Arguments</h1>
359359
<ul>
@@ -365,7 +365,7 @@ <h1>Arguments</h1>
365365
<section id="returns-4" class="level1">
366366
<h1>Returns</h1>
367367
<p>The modified <code>SysDef</code>.</p>
368-
<p>See also: <a href="../../docstrings/medyan.add_fila_type--006e34b8bafba683.html"><code>add_fila_type!</code></a> to add a new filament type with its parameters in one step.</p>
368+
<p>See also: <a href="../../docstrings/medyan.def_fila_type--5a1f6234215ea82d.html"><code>def_fila_type!</code></a> to add a new filament type with its parameters in one step.</p>
369369
</section>
370370
</div>
371371
</div>
@@ -771,7 +771,7 @@ <h3 class="anchored" data-anchor-id="geometry">Geometry</h3>
771771
<h1>Examples</h1>
772772
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb19"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="im">using</span> <span class="bu">MEDYAN</span></span>
773773
<span id="cb19-2"><a href="#cb19-2" aria-hidden="true" tabindex="-1"></a>s <span class="op">=</span> MEDYAN.<span class="fu">SysDef</span>()</span>
774-
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a><span class="fu">add_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>b, <span class="op">:</span>c], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
774+
<span id="cb19-3"><a href="#cb19-3" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>b, <span class="op">:</span>c], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
775775
<span id="cb19-4"><a href="#cb19-4" aria-hidden="true" tabindex="-1"></a></span>
776776
<span id="cb19-5"><a href="#cb19-5" aria-hidden="true" tabindex="-1"></a><span class="co"># Aging: every :a monomer transitions to :b</span></span>
777777
<span id="cb19-6"><a href="#cb19-6" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_reaction!</span>(s;</span>
@@ -889,7 +889,7 @@ <h3 class="anchored" data-anchor-id="rate-2">Rate</h3>
889889
<h1>Examples</h1>
890890
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb21"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb21-1"><a href="#cb21-1" aria-hidden="true" tabindex="-1"></a><span class="im">using</span> <span class="bu">MEDYAN</span></span>
891891
<span id="cb21-2"><a href="#cb21-2" aria-hidden="true" tabindex="-1"></a>s <span class="op">=</span> MEDYAN.<span class="fu">SysDef</span>()</span>
892-
<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a><span class="fu">add_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>plusend, <span class="op">:</span>minusend], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
892+
<span id="cb21-3"><a href="#cb21-3" aria-hidden="true" tabindex="-1"></a><span class="fu">def_fila_type!</span>(s; name<span class="op">=:</span>actin, mono_states<span class="op">=</span>[<span class="op">:</span>a, <span class="op">:</span>plusend, <span class="op">:</span>minusend], param<span class="op">=</span>MEDYAN.ACTIN_TWIST_PARAMS)</span>
893893
<span id="cb21-4"><a href="#cb21-4" aria-hidden="true" tabindex="-1"></a><span class="fu">def_diffusing_species!</span>(s, <span class="op">:</span>actin_mon; coeff<span class="op">=</span><span class="fl">2.5e7</span>)</span>
894894
<span id="cb21-5"><a href="#cb21-5" aria-hidden="true" tabindex="-1"></a></span>
895895
<span id="cb21-6"><a href="#cb21-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Plus-end polymerization: add one monomer (bimolecular with diffusing actin)</span></span>

0 commit comments

Comments
 (0)