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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-09T12:52:22","documenter_version":"1.7.0"}}
{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-09T13:19:04","documenter_version":"1.7.0"}}
10 changes: 5 additions & 5 deletions dev/index.html
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3×3 IdealResidue{Float64}:
-1.06447 -0.199174 1.26364
0.646303 -0.529648 -0.116655
0.0 0.0 0.0</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/ideal.jl#L57-L74">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="ProteinChains.BackboneGeometry" href="#ProteinChains.BackboneGeometry"><code>ProteinChains.BackboneGeometry</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">BackboneGeometry(;
0.0 0.0 0.0</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/ideal.jl#L57-L74">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="ProteinChains.BackboneGeometry" href="#ProteinChains.BackboneGeometry"><code>ProteinChains.BackboneGeometry</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">BackboneGeometry(;
N_Ca_length = 1.46,
Ca_C_length = 1.52,
C_N_length = 1.33,

N_Ca_C_angle = 1.94,
Ca_C_N_angle = 2.03,
C_N_Ca_angle = 2.13,
)</code></pre><p>Define the idealized bond lengths and bond angles of a protein backbone.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/ideal.jl#L1-L13">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="ProteinChains.IdealResidue" href="#ProteinChains.IdealResidue"><code>ProteinChains.IdealResidue</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">IdealResidue{T&lt;:AbstractFloat} &lt;: AbstractMatrix{T}
)</code></pre><p>Define the idealized bond lengths and bond angles of a protein backbone.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/ideal.jl#L1-L13">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="ProteinChains.IdealResidue" href="#ProteinChains.IdealResidue"><code>ProteinChains.IdealResidue</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">IdealResidue{T&lt;:AbstractFloat} &lt;: AbstractMatrix{T}

IdealResidue{T}(backbone_geometry=DEFAULT_BACKBONE_GEOMETRY; template=nothing) where T</code></pre><p>A 3x3 matrix representing the idealized geometry of a protein residue, with columns representing the N, Ca, and C atom positions of a residue positioned at the origin.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/ideal.jl#L26-L33">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="ProteinChains.ProteinChain" href="#ProteinChains.ProteinChain"><code>ProteinChains.ProteinChain</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">ProteinChain{T&lt;:AbstractFloat}</code></pre><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; structure = pdb&quot;1EYE&quot;;
IdealResidue{T}(backbone_geometry=DEFAULT_BACKBONE_GEOMETRY; template=nothing) where T</code></pre><p>A 3x3 matrix representing the idealized geometry of a protein residue, with columns representing the N, Ca, and C atom positions of a residue positioned at the origin.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/ideal.jl#L26-L33">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="ProteinChains.ProteinChain" href="#ProteinChains.ProteinChain"><code>ProteinChains.ProteinChain</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">ProteinChain{T&lt;:AbstractFloat}</code></pre><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; structure = pdb&quot;1EYE&quot;;
[ Info: Downloading file from PDB: 1EYE

julia&gt; structure[1]
Expand All @@ -25,11 +25,11 @@
atoms::Vector{Vector{ProteinChains.Atom{Float64}}} = &lt;field value exceeds max length&gt;
2 properties:
numbering::Vector{Int64} = [5, 6, 7, 8, 9, 10, 11, 12, 13, 14 … 265, 266, 267, 268, 269, 270, 271, 272, 273, 274]
modelnum::Int64 = 1</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/chain.jl#L8-L28">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="ProteinChains.ProteinStructure" href="#ProteinChains.ProteinStructure"><code>ProteinChains.ProteinStructure</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">ProteinStructure{T&lt;:AbstractFloat} &lt;: AbstractVector{ProteinChain{T}}</code></pre><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; pdb&quot;1EYE&quot;
modelnum::Int64 = 1</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/chain.jl#L8-L28">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="ProteinChains.ProteinStructure" href="#ProteinChains.ProteinStructure"><code>ProteinChains.ProteinStructure</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">ProteinStructure{T&lt;:AbstractFloat} &lt;: AbstractVector{ProteinChain{T}}</code></pre><p><strong>Examples</strong></p><pre><code class="language-julia-repl hljs">julia&gt; pdb&quot;1EYE&quot;
1-chain ProteinStructure &quot;1EYE.cif&quot; with 2 dynamic properties:
2 fields:
name::String = &quot;1EYE.cif&quot;
chains::Vector{ProteinChain{Float64}} = &lt;field value exceeds max length&gt;
2 properties:
ids::Vector{String} = [&quot;A&quot;]
lengths::Vector{Int64} = [253]</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/structure.jl#L6-L21">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="ProteinChains.append_residue-Tuple{Backbone, Vector{&lt;:Real}}" href="#ProteinChains.append_residue-Tuple{Backbone, Vector{&lt;:Real}}"><code>ProteinChains.append_residue</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">append_residue(Backbone::Backbone, torsion_angles::Vector{&lt;:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)</code></pre><p>Create a new backbone by appending 3 new torsion angles (ψ, ω, ϕ) at the end, using bond lengths and bond angles specified in <code>BackboneGeometry</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/ideal.jl#L83-L87">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="ProteinChains.prepend_residue-Tuple{Backbone, Vector{&lt;:Real}}" href="#ProteinChains.prepend_residue-Tuple{Backbone, Vector{&lt;:Real}}"><code>ProteinChains.prepend_residue</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">append_residue(Backbone::Backbone, torsion_angles::Vector{&lt;:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)</code></pre><p>Create a new backbone by prepending 3 new torsion angles (ψ, ω, ϕ) at the beginning, using bond lengths and bond angles specified in the <code>BackboneGeometry</code>.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>The torsion angle order is the same as it would be when appending. The order is <em>not</em> reversed.</p></div></div></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/ideal.jl#L95-L102">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="ProteinChains.renumber!-Tuple{ProteinStructure, BioStructures.MMCIFDict}" href="#ProteinChains.renumber!-Tuple{ProteinStructure, BioStructures.MMCIFDict}"><code>ProteinChains.renumber!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">renumber!(structure::ProteinStructure, mmcif_dict::BioStructures.MMCIFDict)</code></pre><p>Renumber the residues in a <code>ProteinStructure</code> object according to the numbering aligned to a reference sequence in the MMCIF file.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/24401775534d6db705cc443d4e7385b2450dfdd1/src/io/renumber.jl#L1-L5">source</a></section></article></article><nav class="docs-footer"><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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Monday 9 September 2024 12:52">Monday 9 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
lengths::Vector{Int64} = [253]</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/structure.jl#L6-L21">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="ProteinChains.append_residue-Tuple{Backbone, Vector{&lt;:Real}}" href="#ProteinChains.append_residue-Tuple{Backbone, Vector{&lt;:Real}}"><code>ProteinChains.append_residue</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">append_residue(Backbone::Backbone, torsion_angles::Vector{&lt;:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)</code></pre><p>Create a new backbone by appending 3 new torsion angles (ψ, ω, ϕ) at the end, using bond lengths and bond angles specified in <code>BackboneGeometry</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/ideal.jl#L83-L87">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="ProteinChains.prepend_residue-Tuple{Backbone, Vector{&lt;:Real}}" href="#ProteinChains.prepend_residue-Tuple{Backbone, Vector{&lt;:Real}}"><code>ProteinChains.prepend_residue</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">append_residue(Backbone::Backbone, torsion_angles::Vector{&lt;:Real}; ideal::BackboneGeometry=DEFAULT_BACKBONE_GEOMETRY)</code></pre><p>Create a new backbone by prepending 3 new torsion angles (ψ, ω, ϕ) at the beginning, using bond lengths and bond angles specified in the <code>BackboneGeometry</code>.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>The torsion angle order is the same as it would be when appending. The order is <em>not</em> reversed.</p></div></div></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/ideal.jl#L95-L102">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="ProteinChains.renumber!-Tuple{ProteinStructure, BioStructures.MMCIFDict}" href="#ProteinChains.renumber!-Tuple{ProteinStructure, BioStructures.MMCIFDict}"><code>ProteinChains.renumber!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">renumber!(structure::ProteinStructure, mmcif_dict::BioStructures.MMCIFDict)</code></pre><p>Renumber the residues in a <code>ProteinStructure</code> object according to the numbering aligned to a reference sequence in the MMCIF file.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/ProteinChains.jl/blob/738d3e6b831cdf9d4f552a3e9744a5d988ac71e6/src/io/renumber.jl#L1-L5">source</a></section></article></article><nav class="docs-footer"><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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Monday 9 September 2024 13:19">Monday 9 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

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