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-<title>medyan.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7 – MEDYAN.jl</title>
+<title>medyan.fila_chem_positions-4bb01f692fdc715c – MEDYAN.jl</title>
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     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#medyan.resolve_all_filament_mesh_crossing" id="toc-medyan.resolve_all_filament_mesh_crossing" class="nav-link active" data-scroll-target="#medyan.resolve_all_filament_mesh_crossing"><code>MEDYAN.resolve_all_filament_mesh_crossing!</code></a>
+  <li><a href="#medyan.fila_chem_positions" id="toc-medyan.fila_chem_positions" class="nav-link active" data-scroll-target="#medyan.fila_chem_positions"><code>MEDYAN.fila_chem_positions</code></a>
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-  <li><a href="#tuple-medyan.context--medyan.binaryaabbtree--169a754d8e383ec5" id="toc-tuple-medyan.context--medyan.binaryaabbtree--169a754d8e383ec5" class="nav-link" data-scroll-target="#tuple-medyan.context--medyan.binaryaabbtree--169a754d8e383ec5"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.BinaryAABBTree}</code></a></li>
+  <li><a href="#tuple-medyan.context--medyan.filaidx--5b8fb92ab95a2b00" id="toc-tuple-medyan.context--medyan.filaidx--5b8fb92ab95a2b00" class="nav-link" data-scroll-target="#tuple-medyan.context--medyan.filaidx--5b8fb92ab95a2b00"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.FilaIdx}</code></a></li>
   </ul></li>
   </ul>
-<div class="toc-actions"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7.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>
+<div class="toc-actions"><ul><li><a href="https://github.com/medyan-dev/MEDYAN.jl/edit/master/quartodocs/docstrings/medyan.fila_chem_positions-4bb01f692fdc715c.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.resolve_all_filament_mesh_crossing" class="level1">
-<h1><code>MEDYAN.resolve_all_filament_mesh_crossing!</code></h1>
-<section id="tuple-medyan.context--medyan.binaryaabbtree--169a754d8e383ec5" class="level2">
-<h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.binaryaabbtree--169a754d8e383ec5"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.BinaryAABBTree}</code></h2>
+<section id="medyan.fila_chem_positions" class="level1">
+<h1><code>MEDYAN.fila_chem_positions</code></h1>
+<section id="tuple-medyan.context--medyan.filaidx--5b8fb92ab95a2b00" class="level2">
+<h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.filaidx--5b8fb92ab95a2b00"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.FilaIdx}</code></h2>
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-<p>Given an AABB tree corresponding to up-to-date membrane mesh triangles, resolve all filament-membrane intersections.</p>
-<p>Requires</p>
-<ul>
-<li>up-to-date unit normals of all triangles in the meshes.</li>
-<li>up-to-date AABB tree corresponding to all membrane meshes.</li>
-</ul>
+<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">fila_chem_positions</span>(</span>
+<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    c<span class="op">::</span><span class="dt">MEDYAN.Context</span>,</span>
+<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    f<span class="op">::</span><span class="dt">MEDYAN.FilaIdx</span></span>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> <span class="dt">Vector</span>{StaticArraysCore.SVector{<span class="fl">3</span>, <span class="dt">Float64</span>}}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>Return a view of the chemistry cylinder endpoint positions for the filament.</p>
+<p>These are the raw positions used for chemistry calculations, at the boundaries between cylinders. Unlike <code>fila_node_positions</code>, the first and last positions are NOT adjusted for partial cylinders or tip extension. Use <code>get_position(c, FilaTipIdx(...))</code> for the actual tip positions. This can be invalid after any mutations to context, so copy if needed.</p>
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@@ -593,4 +628,4 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.binaryaabbtree
 
 
 
-<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.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7.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>
+<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.fila_chem_positions-4bb01f692fdc715c.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>

…ent_mesh_crossing--a8be83a7d2ad65c7.html …ila_chem_positions-4bb01f692fdc715c.htmljulia-docs/dev/docstrings/medyan.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7.html renamed to julia-docs/dev/docstrings/medyan.fila_chem_positions-4bb01f692fdc715c.html julia-docs/dev/docstrings/medyan.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7.html renamed to julia-docs/dev/docstrings/medyan.fila_chem_positions-4bb01f692fdc715c.html

@@ -212,7 +212,8 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.filaidx--5b8fb
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    c<span class="op">::</span><span class="dt">MEDYAN.Context</span>,</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    f<span class="op">::</span><span class="dt">MEDYAN.FilaIdx</span></span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> <span class="dt">Vector</span>{StaticArraysCore.SVector{<span class="fl">3</span>, <span class="dt">Float64</span>}}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
-<p>Return the mechanical node positions of the filament.</p>
+<p>Return the node positions of the filament at cylinder boundaries.</p>
+<p>These are NOT adjusted for tip extension. Use <code>get_position(c, FilaTipIdx(...))</code> to get the tip position with extension applied.</p>
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