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Documenter.jl committed Mar 6, 2024
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T01:02:16","documenter_version":"1.3.0"}}
{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-06T01:02:46","documenter_version":"1.3.0"}}
4 changes: 2 additions & 2 deletions dev/backboner/index.html
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3×12 Backbone{Float64, Matrix{Float64}}:
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/backbone.jl#L3-L43">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.ChainedBonds" href="#Backboner.ChainedBonds"><code>Backboner.ChainedBonds</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">ChainedBonds{T &lt;: Real, V &lt;: AbstractVector{T}}</code></pre><p>A lazy way to store a backbone as a series of bond lengths, angles, and dihedrals. It can be instantiated from a Backbone or a matrix of bond vectors. It can also be used to instantiate a Backbone using the <code>Backbone(bonds::ChainedBonds)</code> constructor.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; backbone = Protein.readpdb(&quot;test/data/1ZAK.pdb&quot;)[&quot;A&quot;].backbone
0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/backbone.jl#L3-L43">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.ChainedBonds" href="#Backboner.ChainedBonds"><code>Backboner.ChainedBonds</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">ChainedBonds{T &lt;: Real, V &lt;: AbstractVector{T}}</code></pre><p>A lazy way to store a backbone as a series of bond lengths, angles, and dihedrals. It can be instantiated from a Backbone or a matrix of bond vectors. It can also be used to instantiate a Backbone using the <code>Backbone(bonds::ChainedBonds)</code> constructor.</p><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; backbone = Protein.readpdb(&quot;test/data/1ZAK.pdb&quot;)[&quot;A&quot;].backbone
3×660 Backbone{Float32, Matrix{Float32}}:
22.346 22.901 23.227 24.115 24.478 25.289 26.091 26.814 … 23.137 22.572 21.48 22.041 21.808 22.263 21.085
17.547 18.031 16.793 16.923 15.779 14.65 14.958 13.827 13.041 14.235 14.668 14.866 13.861 13.862 14.233
23.294 21.993 21.163 20.175 19.336 20.009 21.056 21.652 5.676 5.844 4.974 3.569 2.734 1.355 0.446

julia&gt; bonds = ChainedBonds(backbone)
ChainedBonds{Float32, Vector{Float32}} with 659 bonds, 658 angles, and 657 dihedrals</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/bonds.jl#L66-L85">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.Frame" href="#Backboner.Frame"><code>Backboner.Frame</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Frame{T &lt;: Real}</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/frames.jl#L23-L25">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.Frames" href="#Backboner.Frames"><code>Backboner.Frames</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Frames{T &lt;: Real} &lt;: AbstractVector{Tuple{QuatRotation{T}, Vector{T}}}</code></pre><p>The <code>Frames</code> type is designed to efficiently store and manipulate the rotation and translation of a set of frames.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/frames.jl#L46-L50">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.append_bonds-Tuple{Backbone, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}}" href="#Backboner.append_bonds-Tuple{Backbone, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}}"><code>Backboner.append_bonds</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">append_bonds(backbone, lengths, angles, dihedrals)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/bonds.jl#L193-L195">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.idealize" href="#Backboner.idealize"><code>Backboner.idealize</code></a> — <span class="docstring-category">Function</span></header><section><div><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Zygote must be imported in order to activate the <code>ZygoteIdealizationExt</code> extension, which defines the <code>idealize(::Backbone)</code> method.</p></div></div></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/idealization.jl#L3-L7">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.is_knotted" href="#Backboner.is_knotted"><code>Backboner.is_knotted</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">is_knotted(backbone::Backbone)</code></pre><p>Check if a backbone is knotted.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/2a42325ff5ccccdc5146e11a6a1a461caf507059/src/knots.jl#L92-L96">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../protein/">Protein API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Wednesday 6 March 2024 01:02">Wednesday 6 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
ChainedBonds{Float32, Vector{Float32}} with 659 bonds, 658 angles, and 657 dihedrals</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/bonds.jl#L66-L85">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.Frame" href="#Backboner.Frame"><code>Backboner.Frame</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Frame{T &lt;: Real}</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/frames.jl#L23-L25">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.Frames" href="#Backboner.Frames"><code>Backboner.Frames</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Frames{T &lt;: Real} &lt;: AbstractVector{Tuple{QuatRotation{T}, Vector{T}}}</code></pre><p>The <code>Frames</code> type is designed to efficiently store and manipulate the rotation and translation of a set of frames.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/frames.jl#L46-L50">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.append_bonds-Tuple{Backbone, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}}" href="#Backboner.append_bonds-Tuple{Backbone, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}, AbstractVector{&lt;:Real}}"><code>Backboner.append_bonds</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">append_bonds(backbone, lengths, angles, dihedrals)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/bonds.jl#L193-L195">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.idealize" href="#Backboner.idealize"><code>Backboner.idealize</code></a> — <span class="docstring-category">Function</span></header><section><div><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Zygote must be imported in order to activate the <code>ZygoteIdealizationExt</code> extension, which defines the <code>idealize(::Backbone)</code> method.</p></div></div></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/idealization.jl#L3-L7">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Backboner.is_knotted" href="#Backboner.is_knotted"><code>Backboner.is_knotted</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">is_knotted(backbone::Backbone)</code></pre><p>Check if a backbone is knotted.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/cfec4bff95eb2ea2790f7c264227a5f90d8f6fcd/src/knots.jl#L92-L96">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../protein/">Protein API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Wednesday 6 March 2024 01:02">Wednesday 6 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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