build based on 220c769

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-11-25T15:08:17","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-11-25T15:26:14","documenter_version":"1.1.2"}}

dev/index.html

@@ -17,4 +17,4 @@
 1-element Protein{Float32}:
  Chain A with 220 residues
 
-julia&gt; protein_to_pdb(new_protein, &quot;test/data/1ZAK_A.pdb&quot;);</code></pre><p>The <code>Chain</code> type wraps the <code>Backbone{4}</code> type (4, because it stores the positions of 4 atoms per residue: N, CA, C, O).</p><h2 id="API-Reference"><a class="docs-heading-anchor" href="#API-Reference">API Reference</a><a id="API-Reference-1"></a><a class="docs-heading-anchor-permalink" href="#API-Reference" title="Permalink"></a></h2><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.Backbone" href="#Backboner.Backbone"><code>Backboner.Backbone</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Backbone{N,T}</code></pre><p>A wrapper for a 3xNxL array of coordinates of atoms. Backbone{4} is used to store 3-dimensional coordinates of the backbone atoms (N, CA, C, O) of a protein chain.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/backbone/backbone.jl#L3-L8">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.Chain" href="#Backboner.Chain"><code>Backboner.Chain</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Chain &lt;: AbstractVector{Residue}</code></pre><p>A chain has an identifier (usually a single letter) and holds the backbone atom coordinates, amino acid sequence, and secondary structures of a protein chain. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/chain.jl#L4-L8">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.Protein" href="#Backboner.Protein"><code>Backboner.Protein</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Protein &lt;: AbstractVector{Chain}</code></pre><p>A wrapper for a vector of chains. Chains can be accessed by index or by ID.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/protein.jl#L3-L8">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.add_oxygens-Union{Tuple{Backbone{3, T}}, Tuple{T}} where T&lt;:Real" href="#Backboner.add_oxygens-Union{Tuple{Backbone{3, T}}, Tuple{T}} where T&lt;:Real"><code>Backboner.add_oxygens</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_oxygens(backbone::Backbone{3})</code></pre><p>Add oxygen atoms to the backbone of a protein, turning the coordinate array from size 3x3xL to 3x4xL-1, where L is the length of the backbone.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>One residue is lost in the process, since the orientation of the last oxygen atom cannot be determined. We may consider adding a feature for creating a dummy oxygen atom at the end of the backbone with randomized orientation to preserve the length of the backbone.</p></div></div></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/backbone/oxygen.jl#L50-L60">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.assign_secondary_structure!-Tuple{Protein}" href="#Backboner.assign_secondary_structure!-Tuple{Protein}"><code>Backboner.assign_secondary_structure!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">assign_secondary_structure!(protein)</code></pre><p>Uses a simplified version of DSSP to fill the secondary structure vector of each chain with Loop, Helix, and Strand.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/assign.jl#L5-L9">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.atom_coord_matrix-Tuple{Backbone, Any}" href="#Backboner.atom_coord_matrix-Tuple{Backbone, Any}"><code>Backboner.atom_coord_matrix</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">atom_coord_matrix(backbone, i)</code></pre><p>Returns the coordinates of specific columns of atoms in a backbone.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/coordmatrix.jl#L8-L12">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.backbone_to_locs_and_rots-Union{Tuple{Backbone{N, T}}, Tuple{T}, Tuple{N}, Tuple{Backbone{N, T}, Symbol}} where {N, T}" href="#Backboner.backbone_to_locs_and_rots-Union{Tuple{Backbone{N, T}}, Tuple{T}, Tuple{N}, Tuple{Backbone{N, T}, Symbol}} where {N, T}"><code>Backboner.backbone_to_locs_and_rots</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">backbone_to_locs_and_rots(backbone, unit=:angstrom)</code></pre><p>Returns the locations and rotation matrices of residues in a backbone, according to a defined standard triangle (Backboner.STANDARD<em>TRIANGLE</em>ANGSTROM).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/backbone/rotations.jl#L46-L51">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.locs_and_rots_to_backbone-Union{Tuple{T}, Tuple{AbstractMatrix{T}, AbstractArray{T, 3}}} where T" href="#Backboner.locs_and_rots_to_backbone-Union{Tuple{T}, Tuple{AbstractMatrix{T}, AbstractArray{T, 3}}} where T"><code>Backboner.locs_and_rots_to_backbone</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">locs_and_rots_to_backbone(locations, rot_matrices; unit=:angstrom)</code></pre><p>Returns a backbone with the given locations and rotation matrices of residues. If unit is :nm, the locations are converted to angstroms by multiplying them by 10.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/backbone/rotations.jl#L15-L20">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.pdb_to_protein-Tuple{String}" href="#Backboner.pdb_to_protein-Tuple{String}"><code>Backboner.pdb_to_protein</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">pdb_to_protein(filename::String)</code></pre><p>Assumes that each residue starts with four atoms: N, CA, C, O.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/56b18a96ca63c89176ede4b4739fc23b7fd0d6d9/src/io.jl#L55-L59">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="oxygen/">Oxygen atoms »</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 1.1.2 on <span class="colophon-date" title="Saturday 25 November 2023 15:08">Saturday 25 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; protein_to_pdb(new_protein, &quot;test/data/1ZAK_A.pdb&quot;);</code></pre><p>The <code>Chain</code> type wraps the <code>Backbone{4}</code> type (4, because it stores the positions of 4 atoms per residue: N, CA, C, O).</p><h2 id="API-Reference"><a class="docs-heading-anchor" href="#API-Reference">API Reference</a><a id="API-Reference-1"></a><a class="docs-heading-anchor-permalink" href="#API-Reference" title="Permalink"></a></h2><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.Backbone" href="#Backboner.Backbone"><code>Backboner.Backbone</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Backbone{N,T}</code></pre><p>A wrapper for a 3xNxL array of coordinates of atoms. Backbone{4} is used to store 3-dimensional coordinates of the backbone atoms (N, CA, C, O) of a protein chain.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/backbone/backbone.jl#L3-L8">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.Chain" href="#Backboner.Chain"><code>Backboner.Chain</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Chain &lt;: AbstractVector{Residue}</code></pre><p>A chain has an identifier (usually a single letter) and holds the backbone atom coordinates, amino acid sequence, and secondary structures of a protein chain. </p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/chain.jl#L4-L8">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.Protein" href="#Backboner.Protein"><code>Backboner.Protein</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Protein &lt;: AbstractVector{Chain}</code></pre><p>A wrapper for a vector of chains. Chains can be accessed by index or by ID.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/protein.jl#L3-L8">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.add_oxygens-Union{Tuple{Backbone{3, T}}, Tuple{T}} where T&lt;:Real" href="#Backboner.add_oxygens-Union{Tuple{Backbone{3, T}}, Tuple{T}} where T&lt;:Real"><code>Backboner.add_oxygens</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">add_oxygens(backbone::Backbone{3})</code></pre><p>Add oxygen atoms to the backbone of a protein, turning the coordinate array from size 3x3xL to 3x4xL-1, where L is the length of the backbone.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>One residue is lost in the process, since the orientation of the last oxygen atom cannot be determined. We may consider adding a feature for creating a dummy oxygen atom at the end of the backbone with randomized orientation to preserve the length of the backbone.</p></div></div></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/backbone/oxygen.jl#L50-L60">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.assign_secondary_structure!-Tuple{Protein}" href="#Backboner.assign_secondary_structure!-Tuple{Protein}"><code>Backboner.assign_secondary_structure!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">assign_secondary_structure!(protein)</code></pre><p>Uses a simplified version of DSSP to fill the secondary structure vector of each chain with Loop, Helix, and Strand.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/assign.jl#L5-L9">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.atom_coord_matrix-Tuple{Backbone, Any}" href="#Backboner.atom_coord_matrix-Tuple{Backbone, Any}"><code>Backboner.atom_coord_matrix</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">atom_coord_matrix(backbone, i)</code></pre><p>Returns the coordinates of specific columns of atoms in a backbone.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/coordmatrix.jl#L8-L12">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.backbone_to_locs_and_rots-Union{Tuple{Backbone{N, T}}, Tuple{T}, Tuple{N}, Tuple{Backbone{N, T}, Symbol}} where {N, T}" href="#Backboner.backbone_to_locs_and_rots-Union{Tuple{Backbone{N, T}}, Tuple{T}, Tuple{N}, Tuple{Backbone{N, T}, Symbol}} where {N, T}"><code>Backboner.backbone_to_locs_and_rots</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">backbone_to_locs_and_rots(backbone, unit=:angstrom)</code></pre><p>Returns the locations and rotation matrices of residues in a backbone, according to a defined standard triangle (Backboner.STANDARD<em>TRIANGLE</em>ANGSTROM).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/backbone/rotations.jl#L46-L51">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.locs_and_rots_to_backbone-Union{Tuple{T}, Tuple{AbstractMatrix{T}, AbstractArray{T, 3}}} where T" href="#Backboner.locs_and_rots_to_backbone-Union{Tuple{T}, Tuple{AbstractMatrix{T}, AbstractArray{T, 3}}} where T"><code>Backboner.locs_and_rots_to_backbone</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">locs_and_rots_to_backbone(locations, rot_matrices; unit=:angstrom)</code></pre><p>Returns a backbone with the given locations and rotation matrices of residues. If unit is :nm, the locations are converted to angstroms by multiplying them by 10.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/backbone/rotations.jl#L15-L20">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.pdb_to_protein-Tuple{String}" href="#Backboner.pdb_to_protein-Tuple{String}"><code>Backboner.pdb_to_protein</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">pdb_to_protein(filename::String)</code></pre><p>Assumes that each residue starts with four atoms: N, CA, C, O.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/MurrellGroup/Backboner.jl/blob/220c7696364805f39e09977f0644b5c47e9f9fa9/src/io.jl#L55-L59">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="oxygen/">Oxygen atoms »</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 1.1.2 on <span class="colophon-date" title="Saturday 25 November 2023 15:26">Saturday 25 November 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>