build based on 01f1ed8

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-01-09T20:20:50","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-01-09T21:11:47","documenter_version":"1.2.1"}}

dev/backboner/index.html

@@ -30,7 +30,7 @@
  [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/7158d39f8915f28c234850b0bdf69fe3396dc718/src/backbone.jl#L3-L52">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}</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 = readpdb(&quot;test/data/1ZAK.pdb&quot;)[&quot;A&quot;].backbone
+ [0.0, 0.0, 0.0]</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/01f1ed8748237e0203fd7861d6ddae81fe1ee145/src/backbone.jl#L3-L52">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}</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 = readpdb(&quot;test/data/1ZAK.pdb&quot;)[&quot;A&quot;].backbone
 660-element Backbone{Float32}:
  [22.346, 17.547, 23.294]
  [22.901, 18.031, 21.993]
@@ -43,4 +43,4 @@
  [21.085, 14.233, 0.446]
 
 julia&gt; bonds = ChainedBonds(backbone)
-ChainedBonds{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/7158d39f8915f28c234850b0bdf69fe3396dc718/src/bonds.jl#L92-L117">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/7158d39f8915f28c234850b0bdf69fe3396dc718/src/frames.jl#L7-L11">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/7158d39f8915f28c234850b0bdf69fe3396dc718/src/bonds.jl#L232-L234">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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Tuesday 9 January 2024 20:20">Tuesday 9 January 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ChainedBonds{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/01f1ed8748237e0203fd7861d6ddae81fe1ee145/src/bonds.jl#L92-L117">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/01f1ed8748237e0203fd7861d6ddae81fe1ee145/src/frames.jl#L6-L10">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/01f1ed8748237e0203fd7861d6ddae81fe1ee145/src/bonds.jl#L232-L234">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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Tuesday 9 January 2024 21:11">Tuesday 9 January 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -17,4 +17,4 @@
 1-element Vector{Chain}:
  Chain A with 220 residues
 
-julia&gt; writepdb(new_protein, &quot;test/data/1ZAK_A.pdb&quot;);</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="backboner/">Backboner 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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Tuesday 9 January 2024 20:20">Tuesday 9 January 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; writepdb(new_protein, &quot;test/data/1ZAK_A.pdb&quot;);</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="backboner/">Backboner 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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Tuesday 9 January 2024 21:11">Tuesday 9 January 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>