build based on 772bdea

Author: Documenter.jl

julia-docs/dev/docstrings.html

@@ -224,7 +224,7 @@ <h2 class="anchored" data-anchor-id="union---b2cfd89fb0d1b9c6"><code data-shortc
 <li><p><code>chem_voxel_volumes::Array{Float64, 3}</code>: Volume of each chemical voxel</p></li>
 <li><p><code>chem_voxel_areas::Array{Float64, 4}</code>: Areas of (-x, -y, -z) faces of each chemical voxel</p></li>
 <li><p><code>chem_cylinders::Vector{MEDYAN.ChemCylinders}</code>: Data about filament cylinders, indexed by filament type id</p></li>
-<li><p><code>balls::StructArrays.StructVector{MEDYAN.Ball, @NamedTuple{position::Vector{StaticArraysCore.SVector{3, Float64}}, radius::Vector{Float32}, stiffness::Vector{Float32}, state::Vector{StaticArraysCore.SVector{3, Int64}}}, Int64}</code></p></li>
+<li><p><code>balls::StructArrays.StructVector{MEDYAN.Ball, @NamedTuple{position::Vector{StaticArraysCore.SVector{3, Float64}}, radius::Vector{Float32}, stiffness::Vector{Float32}, state::Vector{StaticArraysCore.SVector{3, Int64}}, is_minimized::Vector{Bool}}, Int64}</code></p></li>
 <li><p><code>membranes::Vector</code>: All membrane meshes.</p></li>
 <li><p><code>next_membid::Ref{MEDYAN.MembId}</code>: Next memb id</p></li>
 <li><p><code>membid2membidx::Dict{MEDYAN.MembId, UInt32}</code>: map from memb id to index memb indexes can change whenever a memb is removed, but id’s are stable</p></li>

julia-docs/dev/docstrings/medyan.context-736368ed32b08894.html

@@ -188,6 +188,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#medyan.is_minimized" id="toc-medyan.is_minimized" class="nav-link active" data-scroll-target="#medyan.is_minimized"><code>MEDYAN.is_minimized</code></a>
   <ul class="collapse">
   <li><a href="#union-tuple-medyan.context--medyan.link---tuple-medyan.context--medyan.link--any---03b671600f22589f" id="toc-union-tuple-medyan.context--medyan.link---tuple-medyan.context--medyan.link--any---03b671600f22589f" class="nav-link" data-scroll-target="#union-tuple-medyan.context--medyan.link---tuple-medyan.context--medyan.link--any---03b671600f22589f"><code data-shortcodes="false">Union{Tuple{MEDYAN.Context, MEDYAN.Link}, Tuple{MEDYAN.Context, MEDYAN.Link, Any}}</code></a></li>
+  <li><a href="#tuple-medyan.context--medyan.ballidx--277715bc057ae4e8" id="toc-tuple-medyan.context--medyan.ballidx--277715bc057ae4e8" class="nav-link" data-scroll-target="#tuple-medyan.context--medyan.ballidx--277715bc057ae4e8"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.BallIdx}</code></a></li>
   <li><a href="#tuple-medyan.context--medyan.filamonoidx--be3f97f8041f5bf1" id="toc-tuple-medyan.context--medyan.filamonoidx--be3f97f8041f5bf1" class="nav-link" data-scroll-target="#tuple-medyan.context--medyan.filamonoidx--be3f97f8041f5bf1"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.FilaMonoIdx}</code></a></li>
   </ul></li>
   </ul>
@@ -215,6 +216,22 @@ <h2 class="anchored" data-anchor-id="union-tuple-medyan.context--medyan.link---t
 </div>
 </div>
 </section>
+<section id="tuple-medyan.context--medyan.ballidx--277715bc057ae4e8" class="level2">
+<h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.ballidx--277715bc057ae4e8"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.BallIdx}</code></h2>
+<div class="callout callout-style-simple callout-note no-icon">
+<div class="callout-body d-flex">
+<div class="callout-icon-container">
+<i class="callout-icon no-icon"></i>
+</div>
+<div class="callout-body-container">
+<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">is_minimized</span>(c<span class="op">::</span><span class="dt">Context</span>, ball<span class="op">::</span><span class="dt">Union{BallIdx, Tag{BallIdx}}</span>)<span class="op">::</span><span class="dt">Bool</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<p>Return <code>true</code> if the ball has been minimized (i.e.&nbsp;its position has been updated by <a href="../docstrings/medyan.minimize_energy--84c4aeab5457d3ee.html"><code>minimize_energy!</code></a> since it was last created or modified).</p>
+<p>Balls are marked as not minimized when created with <a href="../docstrings/medyan.make_ball--ae25720dbd2acec6.html"><code>make_ball!</code></a> or when their <code>position</code> or <code>radius</code> is changed via <a href="../docstrings/medyan.update_ball--83d0c0fbbdbab087.html"><code>update_ball!</code></a>. All balls are marked as minimized at the end of <a href="../docstrings/medyan.minimize_energy--84c4aeab5457d3ee.html"><code>minimize_energy!</code></a>.</p>
+<p>See also: <a href="../docstrings/medyan.make_ball--ae25720dbd2acec6.html"><code>make_ball!</code></a>, <a href="../docstrings/medyan.update_ball--83d0c0fbbdbab087.html"><code>update_ball!</code></a>, <a href="../docstrings/medyan.minimize_energy--84c4aeab5457d3ee.html"><code>minimize_energy!</code></a></p>
+</div>
+</div>
+</div>
+</section>
 <section id="tuple-medyan.context--medyan.filamonoidx--be3f97f8041f5bf1" class="level2">
 <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.filamonoidx--be3f97f8041f5bf1"><code data-shortcodes="false">Tuple{MEDYAN.Context, MEDYAN.FilaMonoIdx}</code></h2>
 <div class="callout callout-style-simple callout-note no-icon">
@@ -223,7 +240,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.filamonoidx--b
 <i class="callout-icon no-icon"></i>
 </div>
 <div class="callout-body-container">
-<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">is_minimized</span>(c<span class="op">::</span><span class="dt">Context</span>, p<span class="op">::</span><span class="dt">Union{FilaMonoIdx, FilaTipIdx, Tag}</span>)<span class="op">::</span><span class="dt">Bool</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<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="fu">is_minimized</span>(c<span class="op">::</span><span class="dt">Context</span>, p<span class="op">::</span><span class="dt">Union{FilaMonoIdx, FilaTipIdx, Tag}</span>)<span class="op">::</span><span class="dt">Bool</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Return true iff the monomer or tip has been minimized. Throw an error if <code>p</code> doesn’t exist.</p>
 </div>
 </div>

julia-docs/dev/docstrings/medyan.is_minimized-ff3858ada5447c46.html

@@ -208,7 +208,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--4896731d1a77eb1c"><co
 <i class="callout-icon no-icon"></i>
 </div>
 <div class="callout-body-container">
-<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">make_ball!</span>(c<span class="op">::</span><span class="dt">Context</span>; position, radius, stiffness<span class="op">=</span><span class="fl">1.0</span>, state<span class="op">=</span>SA[<span class="fl">0</span>,<span class="fl">0</span>,<span class="fl">0</span>]) <span class="op">-&gt;</span> Tag{BallIdx}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<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">make_ball!</span>(c<span class="op">::</span><span class="dt">Context</span>; position, radius, stiffness<span class="op">=</span><span class="fl">1.0f0</span>, state<span class="op">=</span>SA[<span class="fl">0</span>,<span class="fl">0</span>,<span class="fl">0</span>], is_minimized<span class="op">=</span><span class="cn">false</span>) <span class="op">-&gt;</span> Tag{BallIdx}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Create a new ball in <code>c</code> and return a tag for it.</p>
 <section id="keyword-arguments" class="level1">
 <h1>Keyword Arguments</h1>
@@ -217,8 +217,9 @@ <h1>Keyword Arguments</h1>
 <li><code>radius::Float32</code>: Radius of the ball (nm)</li>
 <li><code>stiffness::Float32=1.0</code>: Mechanical stiffness coefficient (pN/nm)</li>
 <li><code>state::SVector{3, Int64}=SA[0,0,0]</code>: Three-component state vector for chemical reactions</li>
+<li><code>is_minimized::Bool=false</code>: Whether the ball is marked as minimized. By default balls are not minimized when created. Set to <code>true</code> to create a ball that is already marked as minimized.</li>
 </ul>
-<p>See also: <a href="../docstrings/medyan.remove_ball--57fbfd7855882ccd.html"><code>remove_ball!</code></a>, <a href="../docstrings/medyan.update_ball--83d0c0fbbdbab087.html"><code>update_ball!</code></a></p>
+<p>See also: <a href="../docstrings/medyan.remove_ball--57fbfd7855882ccd.html"><code>remove_ball!</code></a>, <a href="../docstrings/medyan.update_ball--83d0c0fbbdbab087.html"><code>update_ball!</code></a>, <a href="../docstrings/medyan.get_position-5ca1f4a736664040.html"><code>get_position</code></a>, <a href="../docstrings/medyan.is_minimized-ff3858ada5447c46.html"><code>is_minimized</code></a></p>
 </section>
 </div>
 </div>

julia-docs/dev/docstrings/medyan.make_ball--ae25720dbd2acec6.html

@@ -210,7 +210,7 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.context--medyan.ballidx--27771
 <div class="callout-body-container">
 <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">remove_ball!</span>(c<span class="op">::</span><span class="dt">Context</span>, ball<span class="op">::</span><span class="dt">Union{BallIdx, Tag{BallIdx}}</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Remove a ball from the simulation and unlink all connected links.</p>
-<p>See also: <a href="../docstrings/medyan.make_ball--ae25720dbd2acec6.html"><code>make_ball!</code></a>, <a href="../docstrings/medyan.update_ball--83d0c0fbbdbab087.html"><code>update_ball!</code></a></p>
+<p>See also: <a href="../docstrings/medyan.make_ball--ae25720dbd2acec6.html"><code>make_ball!</code></a>, <a href="../docstrings/medyan.update_ball--83d0c0fbbdbab087.html"><code>update_ball!</code></a>, <a href="../docstrings/medyan.get_position-5ca1f4a736664040.html"><code>get_position</code></a>, <a href="../docstrings/medyan.is_minimized-ff3858ada5447c46.html"><code>is_minimized</code></a></p>
 </div>
 </div>
 </div>

julia-docs/dev/docstrings/medyan.remove_ball--57fbfd7855882ccd.html

@@ -217,8 +217,9 @@ <h1>Keyword Arguments</h1>
 <li><code>radius::Union{Nothing, Float32}=nothing</code>: New radius (nm)</li>
 <li><code>stiffness::Union{Nothing, Float32}=nothing</code>: New stiffness (pN/nm)</li>
 <li><code>state::Union{Nothing, SVector{3, Int64}}=nothing</code>: New state vector</li>
+<li><code>is_minimized::Union{Nothing, Bool}=nothing</code>: Whether the ball is marked as minimized. Defaults to <code>false</code> when <code>position</code> or <code>radius</code> is changed, otherwise unchanged. Set explicitly to override the default behavior.</li>
 </ul>
-<p>See also: <a href="../docstrings/medyan.make_ball--ae25720dbd2acec6.html"><code>make_ball!</code></a>, <a href="../docstrings/medyan.remove_ball--57fbfd7855882ccd.html"><code>remove_ball!</code></a></p>
+<p>See also: <a href="../docstrings/medyan.make_ball--ae25720dbd2acec6.html"><code>make_ball!</code></a>, <a href="../docstrings/medyan.remove_ball--57fbfd7855882ccd.html"><code>remove_ball!</code></a>, <a href="../docstrings/medyan.get_position-5ca1f4a736664040.html"><code>get_position</code></a>, <a href="../docstrings/medyan.is_minimized-ff3858ada5447c46.html"><code>is_minimized</code></a></p>
 </section>
 </div>
 </div>

julia-docs/dev/docstrings/medyan.update_ball--83d0c0fbbdbab087.html

@@ -269,7 +269,7 @@ <h2 class="anchored" data-anchor-id="medyan.context-736368ed32b08894"><a href=".
 <li><p><code>chem_voxel_volumes::Array{Float64, 3}</code>: Volume of each chemical voxel</p></li>
 <li><p><code>chem_voxel_areas::Array{Float64, 4}</code>: Areas of (-x, -y, -z) faces of each chemical voxel</p></li>
 <li><p><code>chem_cylinders::Vector{MEDYAN.ChemCylinders}</code>: Data about filament cylinders, indexed by filament type id</p></li>
-<li><p><code>balls::StructArrays.StructVector{MEDYAN.Ball, @NamedTuple{position::Vector{StaticArraysCore.SVector{3, Float64}}, radius::Vector{Float32}, stiffness::Vector{Float32}, state::Vector{StaticArraysCore.SVector{3, Int64}}}, Int64}</code></p></li>
+<li><p><code>balls::StructArrays.StructVector{MEDYAN.Ball, @NamedTuple{position::Vector{StaticArraysCore.SVector{3, Float64}}, radius::Vector{Float32}, stiffness::Vector{Float32}, state::Vector{StaticArraysCore.SVector{3, Int64}}, is_minimized::Vector{Bool}}, Int64}</code></p></li>
 <li><p><code>membranes::Vector</code>: All membrane meshes.</p></li>
 <li><p><code>next_membid::Ref{MEDYAN.MembId}</code>: Next memb id</p></li>
 <li><p><code>membid2membidx::Dict{MEDYAN.MembId, UInt32}</code>: map from memb id to index memb indexes can change whenever a memb is removed, but id’s are stable</p></li>