build based on 5512482

Author: Documenter.jl

julia-docs/dev/docstrings.html

@@ -236,7 +236,7 @@ <h1>Keyword Arguments</h1>
 <li><p>Required fields:</p>
 <ul>
 <li><code>name::Symbol</code>: Unique identifier for this reaction within the place.</li>
-<li><code>affect!</code>: Callback that executes the reaction. Signature: <code>(c::Context; link::Link, chem_voxel::Int, reaction_id, place_idx, kwargs...) -&gt; Int</code>. <code>link</code> is a handle identifying the specific link instance — pass it to <a href="../docstrings/medyan.get_state-e99d22cacff37374.html"><code>get_state</code></a>, <a href="../docstrings/medyan.update_link--67d413cca6fe82eb.html"><code>update_link!</code></a>, <a href="../docstrings/medyan.link2tags-645330bedbf54254.html"><code>link2tags</code></a>, etc. Return a status code for debugging purposes. For <code>fila_cutoff</code> reactions, also receives <code>place::FilaMonoIdx</code> (a randomly chosen nearby filament monomer within the cutoff distance).</li>
+<li><code>affect!</code>: Callback that executes the reaction. Signature: <code>(c::Context; link::Link, chem_voxel::Int, reaction_id, place_idx, kwargs...) -&gt; Int</code>. <code>link</code> is a handle identifying the specific link instance — pass it to <a href="../docstrings/medyan.get_state-e99d22cacff37374.html"><code>get_state</code></a>, <a href="../docstrings/medyan.update_link--67d413cca6fe82eb.html"><code>update_link!</code></a>, <a href="../docstrings/medyan.link2tags-645330bedbf54254.html"><code>link2tags</code></a>, etc. Return a status code for debugging purposes. For <code>fila_cutoff</code> reactions, also receives <code>place::FilaMonoIdx</code> (a randomly chosen nearby filament monomer within the cutoff distance). For <code>ball_cutoff</code> reactions, also receives <code>place::BallIdx</code> (a randomly chosen nearby ball within the cutoff distance).</li>
 </ul></li>
 <li><p>Optional fields:</p>
 <ul>
@@ -245,7 +245,8 @@ <h1>Keyword Arguments</h1>
 <li><code>invvolumepower::Int64 = 0</code>: Volume scaling. Set to 1 for bimolecular (nm³/s), 0 for unimolecular (1/s).</li>
 <li><code>reactants_extra::String = ""</code>: Additional reactant species whose counts multiply the propensity (e.g., <code>"diffusing.ARP23"</code>). Uses the same <code>"+"</code>-separated format as <a href="../docstrings/medyan.def_reaction--60ae13f69a537c68.html"><code>def_reaction!</code></a> (e.g., <code>"diffusing.A + diffusing.B"</code>).</li>
 <li><code>fila_cutoff::Tuple{Symbol, Float64} = nothing</code>: If set, e.g., <code>(:actin, 50.0)</code>, the propensity is multiplied by the number of nearby filament monomers of that type within the cutoff distance (nm). When the reaction fires, <code>affect!</code> receives one such monomer as <code>place::FilaMonoIdx</code>. <strong>Some monomers are invisible to this search until after a mechanics cycle</strong> — see “Nearby count caching and mechanics” below.</li>
-<li><code>fila_tip_cutoff::Tuple{Symbol, Bool, Float64} = nothing</code>: If set, e.g., <code>(:actin, true, 50.0)</code>, the propensity is multiplied by the number of nearby filament tips of that type within the cutoff distance (nm). The <code>Bool</code> is <code>is_minus_end</code>: <code>true</code> for minus-end tips, <code>false</code> for plus-end tips. When the reaction fires, <code>affect!</code> receives one such tip as <code>place::FilaTipIdx</code>. Mutually exclusive with <code>fila_cutoff</code>. <strong>Some tips are invisible to this search until after a mechanics cycle</strong> — see “Nearby count caching and mechanics” below.</li>
+<li><code>fila_tip_cutoff::Tuple{Symbol, Bool, Float64} = nothing</code>: If set, e.g., <code>(:actin, true, 50.0)</code>, the propensity is multiplied by the number of nearby filament tips of that type within the cutoff distance (nm). The <code>Bool</code> is <code>is_minus_end</code>: <code>true</code> for minus-end tips, <code>false</code> for plus-end tips. When the reaction fires, <code>affect!</code> receives one such tip as <code>place::FilaTipIdx</code>. Mutually exclusive with <code>fila_cutoff</code> and <code>ball_cutoff</code>. <strong>Some tips are invisible to this search until after a mechanics cycle</strong> — see “Nearby count caching and mechanics” below.</li>
+<li><code>ball_cutoff::Float64 = nothing</code>: If set, e.g., <code>50.0</code>, the propensity is multiplied by the number of nearby balls whose centers are within the cutoff distance (nm). When the reaction fires, <code>affect!</code> receives one such ball as <code>place::BallIdx</code>. Only balls that have been through a mechanics cycle (<code>is_minimized</code>) are visible to this search. Mutually exclusive with <code>fila_cutoff</code> and <code>fila_tip_cutoff</code>.</li>
 <li><code>enabled::Bool = true</code>: Whether reaction is active by default.</li>
 </ul></li>
 </ul></li>
@@ -274,9 +275,9 @@ <h1>When rates are reevaluated</h1>
 </ul>
 <p><strong>Workaround — rejection sampling</strong>: If a reaction rate genuinely depends on state that <code>rate</code> cannot track (e.g., the state of a nearby monomer not attached to this link), have <code>rate</code> return an <strong>upper bound</strong> of the true rate. Then in <code>affect!</code>, read the current state and accept the reaction with probability <code>true_rate / upper_bound</code> (rejecting by returning <code>0</code> otherwise). This preserves correct stochastic kinetics despite the stale cache.</p>
 </section>
-<section id="nearby-count-caching-and-mechanics-fila_cutoff-fila_tip_cutoff-reactions" class="level1">
-<h1>Nearby count caching and mechanics (<code>fila_cutoff</code> / <code>fila_tip_cutoff</code> reactions)</h1>
-<p>When a reaction has <code>fila_cutoff</code> set, its total propensity is <code>base_rate × rate(...) × nearby_monomer_count × [reactants_extra counts] / V^invvolumepower</code>. When a reaction has <code>fila_tip_cutoff</code> set, the propensity is the same but with <code>nearby_tip_count</code> in place of <code>nearby_monomer_count</code>. These counts are <strong>cached</strong> alongside the rate factor and have important update semantics:</p>
+<section id="nearby-count-caching-and-mechanics-fila_cutoff-fila_tip_cutoff-ball_cutoff-reactions" class="level1">
+<h1>Nearby count caching and mechanics (<code>fila_cutoff</code> / <code>fila_tip_cutoff</code> / <code>ball_cutoff</code> reactions)</h1>
+<p>When a reaction has <code>fila_cutoff</code> set, its total propensity is <code>base_rate × rate(...) × nearby_monomer_count × [reactants_extra counts] / V^invvolumepower</code>. When a reaction has <code>fila_tip_cutoff</code> set, the propensity is the same but with <code>nearby_tip_count</code> in place of <code>nearby_monomer_count</code>. When a reaction has <code>ball_cutoff</code> set, the propensity is the same but with <code>nearby_ball_count</code> in place of <code>nearby_monomer_count</code>. These counts are <strong>cached</strong> alongside the rate factor and have important update semantics:</p>
 <section id="snapshotted-positions" class="level2">
 <h2 class="anchored" data-anchor-id="snapshotted-positions">Snapshotted positions</h2>
 <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="fl">1</span>. After each mechanics cycle, monomer and tip positions are snapshotted.</span>
@@ -290,7 +291,10 @@ <h2 class="anchored" data-anchor-id="snapshotted-positions">Snapshotted position
 <span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a><span class="fl">4</span>. Similarly, a tip is visible only <span class="cf">if</span> it existed at the last mechanics</span>
 <span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>   snapshot. Polymerization and depolymerization move an existing tip</span>
 <span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a>   but <span class="cf">do</span> not create a <span class="kw">new</span> one, so the tip stays visible at its</span>
-<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>   snapshotted position.</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a>   snapshotted position.</span>
+<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a><span class="fl">5</span>. A ball is visible to <span class="ss">`ball_cutoff`</span> only when</span>
+<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a>   [<span class="ss">`is_minimized`</span>](<span class="pp">@ref</span>) is <span class="ss">`true`</span>. Changing <span class="ss">`position`</span> or <span class="ss">`radius`</span></span>
+<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a>   via [<span class="ss">`update_ball!`</span>](<span class="pp">@ref</span>) resets <span class="ss">`is_minimized`</span> to <span class="ss">`false`</span>.</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 </section>
 </section>
 <section id="example-membrane-bound-npf-cluster" class="level1">

julia-docs/dev/docstrings/medyan.def_link_type--339fe050fe131631.html

@@ -477,7 +477,7 @@ <h1>Keyword Arguments</h1>
 <li><p>Required fields:</p>
 <ul>
 <li><code>name::Symbol</code>: Unique identifier for this reaction within the place.</li>
-<li><code>affect!</code>: Callback that executes the reaction. Signature: <code>(c::Context; link::Link, chem_voxel::Int, reaction_id, place_idx, kwargs...) -&gt; Int</code>. <code>link</code> is a handle identifying the specific link instance — pass it to <a href="../../docstrings/medyan.get_state-e99d22cacff37374.html"><code>get_state</code></a>, <a href="../../docstrings/medyan.update_link--67d413cca6fe82eb.html"><code>update_link!</code></a>, <a href="../../docstrings/medyan.link2tags-645330bedbf54254.html"><code>link2tags</code></a>, etc. Return a status code for debugging purposes. For <code>fila_cutoff</code> reactions, also receives <code>place::FilaMonoIdx</code> (a randomly chosen nearby filament monomer within the cutoff distance).</li>
+<li><code>affect!</code>: Callback that executes the reaction. Signature: <code>(c::Context; link::Link, chem_voxel::Int, reaction_id, place_idx, kwargs...) -&gt; Int</code>. <code>link</code> is a handle identifying the specific link instance — pass it to <a href="../../docstrings/medyan.get_state-e99d22cacff37374.html"><code>get_state</code></a>, <a href="../../docstrings/medyan.update_link--67d413cca6fe82eb.html"><code>update_link!</code></a>, <a href="../../docstrings/medyan.link2tags-645330bedbf54254.html"><code>link2tags</code></a>, etc. Return a status code for debugging purposes. For <code>fila_cutoff</code> reactions, also receives <code>place::FilaMonoIdx</code> (a randomly chosen nearby filament monomer within the cutoff distance). For <code>ball_cutoff</code> reactions, also receives <code>place::BallIdx</code> (a randomly chosen nearby ball within the cutoff distance).</li>
 </ul></li>
 <li><p>Optional fields:</p>
 <ul>
@@ -486,7 +486,8 @@ <h1>Keyword Arguments</h1>
 <li><code>invvolumepower::Int64 = 0</code>: Volume scaling. Set to 1 for bimolecular (nm³/s), 0 for unimolecular (1/s).</li>
 <li><code>reactants_extra::String = ""</code>: Additional reactant species whose counts multiply the propensity (e.g., <code>"diffusing.ARP23"</code>). Uses the same <code>"+"</code>-separated format as <a href="../../docstrings/medyan.def_reaction--60ae13f69a537c68.html"><code>def_reaction!</code></a> (e.g., <code>"diffusing.A + diffusing.B"</code>).</li>
 <li><code>fila_cutoff::Tuple{Symbol, Float64} = nothing</code>: If set, e.g., <code>(:actin, 50.0)</code>, the propensity is multiplied by the number of nearby filament monomers of that type within the cutoff distance (nm). When the reaction fires, <code>affect!</code> receives one such monomer as <code>place::FilaMonoIdx</code>. <strong>Some monomers are invisible to this search until after a mechanics cycle</strong> — see “Nearby count caching and mechanics” below.</li>
-<li><code>fila_tip_cutoff::Tuple{Symbol, Bool, Float64} = nothing</code>: If set, e.g., <code>(:actin, true, 50.0)</code>, the propensity is multiplied by the number of nearby filament tips of that type within the cutoff distance (nm). The <code>Bool</code> is <code>is_minus_end</code>: <code>true</code> for minus-end tips, <code>false</code> for plus-end tips. When the reaction fires, <code>affect!</code> receives one such tip as <code>place::FilaTipIdx</code>. Mutually exclusive with <code>fila_cutoff</code>. <strong>Some tips are invisible to this search until after a mechanics cycle</strong> — see “Nearby count caching and mechanics” below.</li>
+<li><code>fila_tip_cutoff::Tuple{Symbol, Bool, Float64} = nothing</code>: If set, e.g., <code>(:actin, true, 50.0)</code>, the propensity is multiplied by the number of nearby filament tips of that type within the cutoff distance (nm). The <code>Bool</code> is <code>is_minus_end</code>: <code>true</code> for minus-end tips, <code>false</code> for plus-end tips. When the reaction fires, <code>affect!</code> receives one such tip as <code>place::FilaTipIdx</code>. Mutually exclusive with <code>fila_cutoff</code> and <code>ball_cutoff</code>. <strong>Some tips are invisible to this search until after a mechanics cycle</strong> — see “Nearby count caching and mechanics” below.</li>
+<li><code>ball_cutoff::Float64 = nothing</code>: If set, e.g., <code>50.0</code>, the propensity is multiplied by the number of nearby balls whose centers are within the cutoff distance (nm). When the reaction fires, <code>affect!</code> receives one such ball as <code>place::BallIdx</code>. Only balls that have been through a mechanics cycle (<code>is_minimized</code>) are visible to this search. Mutually exclusive with <code>fila_cutoff</code> and <code>fila_tip_cutoff</code>.</li>
 <li><code>enabled::Bool = true</code>: Whether reaction is active by default.</li>
 </ul></li>
 </ul></li>
@@ -515,9 +516,9 @@ <h1>When rates are reevaluated</h1>
 </ul>
 <p><strong>Workaround — rejection sampling</strong>: If a reaction rate genuinely depends on state that <code>rate</code> cannot track (e.g., the state of a nearby monomer not attached to this link), have <code>rate</code> return an <strong>upper bound</strong> of the true rate. Then in <code>affect!</code>, read the current state and accept the reaction with probability <code>true_rate / upper_bound</code> (rejecting by returning <code>0</code> otherwise). This preserves correct stochastic kinetics despite the stale cache.</p>
 </section>
-<section id="nearby-count-caching-and-mechanics-fila_cutoff-fila_tip_cutoff-reactions" class="level1">
-<h1>Nearby count caching and mechanics (<code>fila_cutoff</code> / <code>fila_tip_cutoff</code> reactions)</h1>
-<p>When a reaction has <code>fila_cutoff</code> set, its total propensity is <code>base_rate × rate(...) × nearby_monomer_count × [reactants_extra counts] / V^invvolumepower</code>. When a reaction has <code>fila_tip_cutoff</code> set, the propensity is the same but with <code>nearby_tip_count</code> in place of <code>nearby_monomer_count</code>. These counts are <strong>cached</strong> alongside the rate factor and have important update semantics:</p>
+<section id="nearby-count-caching-and-mechanics-fila_cutoff-fila_tip_cutoff-ball_cutoff-reactions" class="level1">
+<h1>Nearby count caching and mechanics (<code>fila_cutoff</code> / <code>fila_tip_cutoff</code> / <code>ball_cutoff</code> reactions)</h1>
+<p>When a reaction has <code>fila_cutoff</code> set, its total propensity is <code>base_rate × rate(...) × nearby_monomer_count × [reactants_extra counts] / V^invvolumepower</code>. When a reaction has <code>fila_tip_cutoff</code> set, the propensity is the same but with <code>nearby_tip_count</code> in place of <code>nearby_monomer_count</code>. When a reaction has <code>ball_cutoff</code> set, the propensity is the same but with <code>nearby_ball_count</code> in place of <code>nearby_monomer_count</code>. These counts are <strong>cached</strong> alongside the rate factor and have important update semantics:</p>
 <section id="snapshotted-positions" class="level2">
 <h2 class="anchored" data-anchor-id="snapshotted-positions">Snapshotted positions</h2>
 <div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb12"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="fl">1</span>. After each mechanics cycle, monomer and tip positions are snapshotted.</span>
@@ -531,7 +532,10 @@ <h2 class="anchored" data-anchor-id="snapshotted-positions">Snapshotted position
 <span id="cb12-9"><a href="#cb12-9" aria-hidden="true" tabindex="-1"></a><span class="fl">4</span>. Similarly, a tip is visible only <span class="cf">if</span> it existed at the last mechanics</span>
 <span id="cb12-10"><a href="#cb12-10" aria-hidden="true" tabindex="-1"></a>   snapshot. Polymerization and depolymerization move an existing tip</span>
 <span id="cb12-11"><a href="#cb12-11" aria-hidden="true" tabindex="-1"></a>   but <span class="cf">do</span> not create a <span class="kw">new</span> one, so the tip stays visible at its</span>
-<span id="cb12-12"><a href="#cb12-12" aria-hidden="true" tabindex="-1"></a>   snapshotted position.</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<span id="cb12-12"><a href="#cb12-12" aria-hidden="true" tabindex="-1"></a>   snapshotted position.</span>
+<span id="cb12-13"><a href="#cb12-13" aria-hidden="true" tabindex="-1"></a><span class="fl">5</span>. A ball is visible to <span class="ss">`ball_cutoff`</span> only when</span>
+<span id="cb12-14"><a href="#cb12-14" aria-hidden="true" tabindex="-1"></a>   [<span class="ss">`is_minimized`</span>](<span class="pp">@ref</span>) is <span class="ss">`true`</span>. Changing <span class="ss">`position`</span> or <span class="ss">`radius`</span></span>
+<span id="cb12-15"><a href="#cb12-15" aria-hidden="true" tabindex="-1"></a>   via [<span class="ss">`update_ball!`</span>](<span class="pp">@ref</span>) resets <span class="ss">`is_minimized`</span> to <span class="ss">`false`</span>.</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 </section>
 </section>
 <section id="example-membrane-bound-npf-cluster" class="level1">