build based on 54ef21c

Author: Documenter.jl

julia-docs/dev/docstrings.html

@@ -180,6 +180,8 @@ <h2 class="anchored" data-anchor-id="union---b2cfd89fb0d1b9c6"><code data-shortc
 <p><code>E = 1//2 * relu(pos ⋅ planes[bi][1:3] - planes[bi][4])^2</code></p>
 <p>For example, a mech bounding plane <code>[1,0,0,3]</code> would try and make x &lt; 3 nm with a spring constant of 1 pN/nm.</p>
 <p><code>2.0*[1,0,0,3]</code> would try and make x &lt; 3 nm with a spring constant of 4 pN/nm.</p></li>
+<li><p><code>plane_layers::Vector{UInt32}</code>: Collision layers for each plane. Default: UInt32(1).</p></li>
+<li><p><code>plane_ncmask::Vector{UInt32}</code>: No-collide mask for each plane. Default: UInt32(0) (collide with all layers).</p></li>
 <li><p><code>capsules::Vector{StaticArraysCore.SVector{8, Float64}}</code>: Capsules that make up the mechanical boundary of the simulation.</p>
 <p><code>capsules[bi][1:3]</code> is the starting point of the spine line segment (nm). <code>capsules[bi][4:6]</code> is the axis of the spine line segment (nm). <code>capsules[bi][7]</code> is the radius (nm). If the radius is negative, the domain is the outside of the capsule, if the radius is positive the domain is inside the capsule. <code>capsules[bi][8]</code> is the spring constant (pN/nm).</p>
 <p>if <code>capsules[bi][4:6]</code> is zero then the capsule is a sphere. Capsule boundaries can be combined with plane boundaries to create cylinder boundaries.</p>
@@ -189,6 +191,8 @@ <h2 class="anchored" data-anchor-id="union---b2cfd89fb0d1b9c6"><code data-shortc
 <li>r0 is capsules[bi][7]</li>
 <li>k is capsules[bi][8]</li>
 </ul></li>
+<li><p><code>capsule_layers::Vector{UInt32}</code>: Collision layers for each capsule. Default: UInt32(1).</p></li>
+<li><p><code>capsule_ncmask::Vector{UInt32}</code>: No-collide mask for each capsule. Default: UInt32(0) (collide with all layers).</p></li>
 </ul>
 </div>
 </div>

julia-docs/dev/docstrings/medyan.boundary-f1e7be79002a27f8.html

@@ -211,8 +211,10 @@ <h2 class="anchored" data-anchor-id="tuple-medyan.cubicgrid--0971be2da0774049"><
 <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">boundary_box</span>(</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>    grid<span class="op">::</span><span class="dt">MEDYAN.CubicGrid</span>;</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    offset,</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    stiffness</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    stiffness,</span>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    collision_layers,</span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    no_collide_mask</span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Return a box boundary at the edge of a grid.</p>
 <p><code>offset</code>(nm): How far the bounding planes should be moved in from the edge of the grid. Positive is inside the grid, negative is outside the grid.</p>
 <p><code>stiffness</code>(pN/nm): How strong the boundary is.</p>

julia-docs/dev/docstrings/medyan.boundary_box-060d4c56df40146a.html

@@ -213,8 +213,10 @@ <h2 class="anchored" data-anchor-id="tuple---3937a4f1811c9dc1"><code data-shortc
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    center,</span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    axis,</span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    radius,</span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    stiffness</span>
-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    stiffness,</span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>    collision_layers,</span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>    no_collide_mask</span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Return a capsule boundary.</p>
 <p><code>center</code>(nm): The center of the capsule.</p>
 <p><code>axis</code>(nm): The direction and length of the capsule spine. The spine line segment goes from <code>center - axis/2</code> to <code>center + axis/2</code> If zero the capsule is a sphere.</p>

julia-docs/dev/docstrings/medyan.boundary_capsule-1700142f310bd9db.html

@@ -213,8 +213,10 @@ <h2 class="anchored" data-anchor-id="tuple---3937a4f1811c9dc1"><code data-shortc
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    center,</span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    axis,</span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    radius,</span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    stiffness</span>
-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    stiffness,</span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>    collision_layers,</span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>    no_collide_mask</span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Return a cylinder boundary.</p>
 <p><code>center</code>(nm): The center of the cylinder.</p>
 <p><code>axis</code>(nm): The direction and length of the cylinder. The spine line segment goes from <code>center - axis/2</code> to <code>center + axis/2</code> the full length of the cylinder is <code>norm(axis)</code>.</p>

julia-docs/dev/docstrings/medyan.boundary_cylinder-33a45da15f9672d3.html

@@ -212,8 +212,10 @@ <h2 class="anchored" data-anchor-id="tuple---3937a4f1811c9dc1"><code data-shortc
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>;</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>    normal,</span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    point,</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    stiffness</span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
+<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    stiffness,</span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>    collision_layers,</span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a>    no_collide_mask</span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>) <span class="op">-&gt;</span> MEDYAN.Boundary</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <p>Return a plane boundary.</p>
 <p><code>normal</code>(unit vector): Vector pointing normal to the plane. This points outside of the boundary.</p>
 <p><code>point</code>(nm): Point on the plane.</p>

julia-docs/dev/docstrings/medyan.boundary_plane-2caa9b52b3b3f0cc.html

@@ -226,7 +226,7 @@ <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}}, is_minimized::Vector{Bool}}, 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}, collision_layers::Vector{UInt32}, no_collide_mask::Vector{UInt32}, state::Vector{StaticArraysCore.SVector{3, Int64}}, is_minimized::Vector{Bool}}, Int64}</code></p></li>
 <li><p><code>ball_cell_list_cache::Union{Nothing, MEDYAN.PointCellList}</code>: Cached PointCellList for minimized ball positions. <code>nothing</code> means cache is invalid.</p></li>
 <li><p><code>ball_cell_list_grid_spacing::Float32</code>: Grid spacing (nm) for the ball PointCellList. Default is 100 nm.</p></li>
 <li><p><code>membranes::Vector</code>: All membrane meshes.</p></li>

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

@@ -183,6 +183,8 @@ <h2 class="anchored" data-anchor-id="union---b2cfd89fb0d1b9c6"><code data-shortc
 <li><code>twist_per_monomer::Float64</code>: Twist between monomers (rad)</li>
 <li><code>numpercylinder::Int32</code>: Number of monomers per cylinder</li>
 <li><code>kcollide::Float64</code>: Repulsion stiffness (pN/nm)</li>
+<li><code>collision_layers::UInt32</code>: Collision layers bitmask. Defines which layers this filament type is on.</li>
+<li><code>no_collide_mask::UInt32</code>: No-collide mask bitmask. Bits set = layers this filament type will not collide with.</li>
 <li><code>max_num_unmin_end::Int32</code>: Maximum number of unminimized monomers that can be on an end. This should be less than the minimum <code>radius</code> of other filaments + <code>radius</code> divided by <code>spacing</code>.</li>
 </ul>
 </div>

julia-docs/dev/docstrings/medyan.filamentmechparams-003aa222b98c6481.html

@@ -208,14 +208,16 @@ <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">1.0f0</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>
+<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>, collision_layers<span class="op">=</span><span class="fu">UInt32</span>(<span class="fl">1</span>), no_collide_mask<span class="op">=</span><span class="fu">UInt32</span>(<span class="fl">0</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>
 <ul>
 <li><code>position::SVector{3, Float64}</code>: 3D position of the ball center (nm)</li>
 <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>collision_layers::UInt32=UInt32(1)</code>: Collision layers bitmask. Defines which layers this ball is on.</li>
+<li><code>no_collide_mask::UInt32=UInt32(0)</code>: No-collide mask bitmask. Bits set = layers this ball will not collide with.</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>

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

@@ -216,6 +216,8 @@ <h1>Keyword Arguments</h1>
 <li><code>position::Union{Nothing, SVector{3, Float64}}=nothing</code>: New position (nm)</li>
 <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>collision_layers::Union{Nothing, UInt32}=nothing</code>: New collision layers bitmask</li>
+<li><code>no_collide_mask::Union{Nothing, UInt32}=nothing</code>: New no-collide mask bitmask</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>