build based on 204f5e4

Author: Documenter.jl

julia-docs/dev/docstrings.html

@@ -216,8 +216,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.filatipidx--d5
 <p>The extension controls how far the tip position extends outward from the last monomer center. It affects both the chemistry tip position ([<code>get_position</code>] for <code>FilaTipIdx</code>) and the mechanical endpoint used in energy minimization (volume exclusion, equilibrium length):</p>
 <ul>
 <li><code>0.0</code>: tip at the monomer center</li>
-<li><code>DEFAULT_TIP_EXTENSION</code> (0.5): tip at the node boundary (default, backwards compatible)</li>
-<li><code>&gt; 0.5</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
+<li><code>&gt; 0.0</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
 <li><code>&lt; 0.0</code>: tip moves inward past the monomer center</li>
 </ul>
 <p>The mechanical node positions (<a href="../docstrings/medyan.fila_node_positions-f4c5bac0dcb570ff.html"><code>fila_node_positions</code></a>) remain at cylinder boundaries and are not affected by the extension.</p>

julia-docs/dev/docstrings/medyan.fila_tip_extension-cef965509800f1e7.html

@@ -226,8 +226,8 @@ <h1>Keyword Arguments</h1>
 <li><p><code>minus_end_mat_dir=nothing</code>: <code>SVector{3,Float64}</code>. The mat direction of the minus end node.</p></li>
 <li><p><code>joint_twists=nothing</code>: <code>Collection of</code>Float64`. The extra material frame axial rotation at the joints between the cylinders.</p></li>
 <li><p><code>tip_load_forces=(0.0=&gt;0.0)</code>: tip load forces, usually don’t use this, because load forces will automatically get updated at the next minimization.</p></li>
-<li><p><code>minus_tip_extension=0.5</code>: tip extension for the minus end in monomer spacings. 0=monomer center, DEFAULT<em>TIP</em>EXTENSION=node boundary (default). See <a href="../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
-<li><p><code>plus_tip_extension=0.5</code>: tip extension for the plus end in monomer spacings. 0=monomer center, DEFAULT<em>TIP</em>EXTENSION=node boundary (default). See <a href="../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
+<li><p><code>minus_tip_extension=0.0</code>: tip extension for the minus end in monomer spacings. 0=monomer center. See <a href="../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
+<li><p><code>plus_tip_extension=0.0</code>: tip extension for the plus end in monomer spacings. 0=monomer center. See <a href="../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
 </ul>
 </section>
 </div>

julia-docs/dev/docstrings/medyan.get_beta-22a7f89896ccffb6.html

@@ -213,8 +213,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.filatipidx--fl
 <p>The extension controls how far the tip position extends outward from the last monomer center. It affects both the chemistry tip position ([<code>get_position</code>] for <code>FilaTipIdx</code>) and the mechanical endpoint used in energy minimization (volume exclusion, equilibrium length):</p>
 <ul>
 <li><code>0.0</code>: tip at the monomer center</li>
-<li><code>DEFAULT_TIP_EXTENSION</code> (0.5): tip at the node boundary (default, backwards compatible)</li>
-<li><code>&gt; 0.5</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
+<li><code>&gt; 0.0</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
 <li><code>&lt; 0.0</code>: tip moves inward past the monomer center</li>
 </ul>
 <p>The mechanical node positions (<a href="../docstrings/medyan.fila_node_positions-f4c5bac0dcb570ff.html"><code>fila_node_positions</code></a>) remain at cylinder boundaries and are not affected by the extension. During energy minimization, end nodes are temporarily shifted to tip positions so volume exclusion sees the extension, then shifted back afterward.</p>

julia-docs/dev/docstrings/medyan.make_fila--f2346a40b4792de5.html

@@ -483,8 +483,7 @@ <h2 class="anchored" data-anchor-id="medyan.fila_tip_extension-cef965509800f1e7"
 <p>The extension controls how far the tip position extends outward from the last monomer center. It affects both the chemistry tip position ([<code>get_position</code>] for <code>FilaTipIdx</code>) and the mechanical endpoint used in energy minimization (volume exclusion, equilibrium length):</p>
 <ul>
 <li><code>0.0</code>: tip at the monomer center</li>
-<li><code>DEFAULT_TIP_EXTENSION</code> (0.5): tip at the node boundary (default, backwards compatible)</li>
-<li><code>&gt; 0.5</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
+<li><code>&gt; 0.0</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
 <li><code>&lt; 0.0</code>: tip moves inward past the monomer center</li>
 </ul>
 <p>The mechanical node positions (<a href="../../../docstrings/medyan.fila_node_positions-f4c5bac0dcb570ff.html"><code>fila_node_positions</code></a>) remain at cylinder boundaries and are not affected by the extension.</p>

julia-docs/dev/docstrings/medyan.set_fila_tip_extension--4067d098840cde42.html

@@ -226,8 +226,8 @@ <h1>Keyword Arguments</h1>
 <li><p><code>minus_end_mat_dir=nothing</code>: <code>SVector{3,Float64}</code>. The mat direction of the minus end node.</p></li>
 <li><p><code>joint_twists=nothing</code>: <code>Collection of</code>Float64`. The extra material frame axial rotation at the joints between the cylinders.</p></li>
 <li><p><code>tip_load_forces=(0.0=&gt;0.0)</code>: tip load forces, usually don’t use this, because load forces will automatically get updated at the next minimization.</p></li>
-<li><p><code>minus_tip_extension=0.5</code>: tip extension for the minus end in monomer spacings. 0=monomer center, DEFAULT<em>TIP</em>EXTENSION=node boundary (default). See <a href="../../../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
-<li><p><code>plus_tip_extension=0.5</code>: tip extension for the plus end in monomer spacings. 0=monomer center, DEFAULT<em>TIP</em>EXTENSION=node boundary (default). See <a href="../../../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
+<li><p><code>minus_tip_extension=0.0</code>: tip extension for the minus end in monomer spacings. 0=monomer center. See <a href="../../../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
+<li><p><code>plus_tip_extension=0.0</code>: tip extension for the plus end in monomer spacings. 0=monomer center. See <a href="../../../docstrings/medyan.fila_tip_extension-cef965509800f1e7.html"><code>fila_tip_extension</code></a>.</p></li>
 </ul>
 </section>
 </div>

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

@@ -213,8 +213,7 @@ <h2 class="anchored" data-anchor-id="medyan.set_fila_tip_extension--4067d098840c
 <p>The extension controls how far the tip position extends outward from the last monomer center. It affects both the chemistry tip position ([<code>get_position</code>] for <code>FilaTipIdx</code>) and the mechanical endpoint used in energy minimization (volume exclusion, equilibrium length):</p>
 <ul>
 <li><code>0.0</code>: tip at the monomer center</li>
-<li><code>DEFAULT_TIP_EXTENSION</code> (0.5): tip at the node boundary (default, backwards compatible)</li>
-<li><code>&gt; 0.5</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
+<li><code>&gt; 0.0</code>: tip extends further outward (e.g.&nbsp;bulky end-binding protein)</li>
 <li><code>&lt; 0.0</code>: tip moves inward past the monomer center</li>
 </ul>
 <p>The mechanical node positions (<a href="../../../docstrings/medyan.fila_node_positions-f4c5bac0dcb570ff.html"><code>fila_node_positions</code></a>) remain at cylinder boundaries and are not affected by the extension. During energy minimization, end nodes are temporarily shifted to tip positions so volume exclusion sees the extension, then shifted back afterward.</p>

julia-docs/dev/docstrings/src/filament/functions.html

@@ -79,6 +79,7 @@
       "/docstrings/medyan.filter_grididat-58a94154d21e32b0.html",
       "/docstrings/medyan.get_all_links-fe0d12c0df825f7e.html",
       "/docstrings/medyan.get_all_tags-3a8e6bc0634c8a4d.html",
+      "/docstrings/medyan.get_beta-22a7f89896ccffb6.html",
       "/docstrings/medyan.get_bond_enabled-c3461fb32deb4276.html",
       "/docstrings/medyan.get_bond_states-b314ae6ee2a2b3cf.html",
       "/docstrings/medyan.get_chem_boundary_grid_spacing-3726877b3aae3a2e.html",