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{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-06-04T10:51:08","documenter_version":"1.4.1"}}
{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-06-04T10:53:46","documenter_version":"1.4.1"}}
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Overview · Backboner.jl</title><meta name="title" content="Overview · Backboner.jl"/><meta property="og:title" content="Overview · Backboner.jl"/><meta property="twitter:title" content="Overview · Backboner.jl"/><meta name="description" content="Documentation for Backboner.jl."/><meta property="og:description" content="Documentation for Backboner.jl."/><meta property="twitter:description" content="Documentation for Backboner.jl."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>Backboner.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Overview</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li><li><a class="tocitem" href="#Example-usage"><span>Example usage</span></a></li></ul></li><li><a class="tocitem" href="backboner/">Backboner API</a></li><li><a class="tocitem" href="protein/">Protein API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Overview</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Overview</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/MurrellGroup/Backboner.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/MurrellGroup/Backboner.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Backboner"><a class="docs-heading-anchor" href="#Backboner">Backboner</a><a id="Backboner-1"></a><a class="docs-heading-anchor-permalink" href="#Backboner" title="Permalink"></a></h1><p><a href="https://github.com/MurrellGroup/Backboner.jl/releases/latest"><img src="https://img.shields.io/github/release/MurrellGroup/Backboner.jl.svg" alt="Latest Release"/></a> <a href="https://opensource.org/license/MIT"><img src="https://img.shields.io/badge/license-MIT-green.svg" alt="MIT license"/></a> <a href="https://MurrellGroup.github.io/Backboner.jl/stable/"><img src="https://img.shields.io/badge/docs-stable-blue.svg" alt="Documentation"/></a> <a href="https://MurrellGroup.github.io/Backboner.jl/dev/"><img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Documentation"/></a> <a href="https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml?query=branch%3Amain"><img src="https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml/badge.svg?branch=main" alt="Build Status"/></a> <a href="https://codecov.io/gh/MurrellGroup/Backboner.jl"><img src="https://codecov.io/gh/MurrellGroup/Backboner.jl/branch/main/graph/badge.svg" alt="Coverage"/></a></p><p>Backboner is a Julia package that offers a set of types and functions for working with molecular <em>backbones</em>: defined here as continuous chains of bonded atoms.<sup class="footnote-reference"><a id="citeref-1" href="#footnote-1">[1]</a></sup> The package provides a few different types for representing backbones:</p><ul><li><code>Backbone</code>: a type containing a 3xN matrix of coordinates</li><li><code>ChainedBonds</code>: a type that holds vectors of bond lengths, bond angles, and dihedral angles</li><li><code>Frames</code>: a collection of rotations and translations (e.g. for representing orientations and locations of protein residues)</li></ul><p>The <code>Protein</code> submodule contains functions and types for working specifically with proteins. A protein can be loaded from a PDB file using the <code>Backboner.Protein.readpdb</code> function, which returns a <code>Vector{Backboner.Protein.Chain}</code>. Conversely, a <code>Vector{Backboner.Protein.Chain}</code> instance can be written to a PDB file using the <code>writepdb</code> function.</p><p><a href="https://github.com/MurrellGroup/Backboner.jl">View the source code on GitHub</a> (licensed under MIT).</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Backboner is registered, and can be installed in the Julia REPL. Press <code>]</code> to enter pkg mode, and then run:</p><pre><code class="nohighlight hljs">add Backboner</code></pre><h2 id="Example-usage"><a class="docs-heading-anchor" href="#Example-usage">Example usage</a><a id="Example-usage-1"></a><a class="docs-heading-anchor-permalink" href="#Example-usage" title="Permalink"></a></h2><pre><code class="language-julia hljs">julia&gt; using Backboner, Backboner.Protein
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Overview · Backboner.jl</title><meta name="title" content="Overview · Backboner.jl"/><meta property="og:title" content="Overview · Backboner.jl"/><meta property="twitter:title" content="Overview · Backboner.jl"/><meta name="description" content="Documentation for Backboner.jl."/><meta property="og:description" content="Documentation for Backboner.jl."/><meta property="twitter:description" content="Documentation for Backboner.jl."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>Backboner.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Overview</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li><li><a class="tocitem" href="#Example-usage"><span>Example usage</span></a></li></ul></li><li><a class="tocitem" href="backboner/">Backboner API</a></li><li><a class="tocitem" href="protein/">Protein API</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Overview</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Overview</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/MurrellGroup/Backboner.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/MurrellGroup/Backboner.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Backboner"><a class="docs-heading-anchor" href="#Backboner">Backboner</a><a id="Backboner-1"></a><a class="docs-heading-anchor-permalink" href="#Backboner" title="Permalink"></a></h1><p><a href="https://github.com/MurrellGroup/Backboner.jl/releases/latest"><img src="https://img.shields.io/github/release/MurrellGroup/Backboner.jl.svg" alt="Latest Release"/></a> <a href="https://opensource.org/license/MIT"><img src="https://img.shields.io/badge/license-MIT-green.svg" alt="MIT license"/></a> <a href="https://MurrellGroup.github.io/Backboner.jl/dev/"><img src="https://img.shields.io/badge/docs-latest-blue.svg" alt="Documentation"/></a> <a href="https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml?query=branch%3Amain"><img src="https://github.com/MurrellGroup/Backboner.jl/actions/workflows/CI.yml/badge.svg?branch=main" alt="Build Status"/></a> <a href="https://codecov.io/gh/MurrellGroup/Backboner.jl"><img src="https://codecov.io/gh/MurrellGroup/Backboner.jl/branch/main/graph/badge.svg" alt="Coverage"/></a></p><p>Backboner is a Julia package that offers a set of types and functions for working with molecular <em>backbones</em>: defined here as continuous chains of bonded atoms.<sup class="footnote-reference"><a id="citeref-1" href="#footnote-1">[1]</a></sup> The package provides a few different types for representing backbones:</p><ul><li><code>Backbone</code>: a type containing a 3xN matrix of coordinates</li><li><code>ChainedBonds</code>: a type that holds vectors of bond lengths, bond angles, and dihedral angles</li><li><code>Frames</code>: a collection of rotations and translations (e.g. for representing orientations and locations of protein residues)</li></ul><p>The <code>Protein</code> submodule contains functions and types for working specifically with proteins. A protein can be loaded from a PDB file using the <code>Backboner.Protein.readpdb</code> function, which returns a <code>Vector{Backboner.Protein.Chain}</code>. Conversely, a <code>Vector{Backboner.Protein.Chain}</code> instance can be written to a PDB file using the <code>writepdb</code> function.</p><p><a href="https://github.com/MurrellGroup/Backboner.jl">View the source code on GitHub</a> (licensed under MIT).</p><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Backboner is registered, and can be installed in the Julia REPL. Press <code>]</code> to enter pkg mode, and then run:</p><pre><code class="nohighlight hljs">add Backboner</code></pre><h2 id="Example-usage"><a class="docs-heading-anchor" href="#Example-usage">Example usage</a><a id="Example-usage-1"></a><a class="docs-heading-anchor-permalink" href="#Example-usage" title="Permalink"></a></h2><pre><code class="language-julia hljs">julia&gt; using Backboner, Backboner.Protein

julia&gt; chains = readpdb(&quot;test/data/1ZAK.pdb&quot;)
2-element Vector{Chain}:
Chain A with 220 residues
Chain B with 220 residues

julia&gt; backbone = chains[1].backbone
3×660 Backbone{Float32, Matrix{Float32}}:
22.346 22.901 23.227 24.115 24.478 … 21.48 22.041 21.808 22.263 21.085
17.547 18.031 16.793 16.923 15.779 14.668 14.866 13.861 13.862 14.233
23.294 21.993 21.163 20.175 19.336 4.974 3.569 2.734 1.355 0.446
660-element Backbone{Float32, Matrix{Float32}}:
[22.346, 17.547, 23.294]
[22.901, 18.031, 21.993]
[23.227, 16.793, 21.163]
[24.115, 16.923, 20.175]
[24.478, 15.779, 19.336]
⋮
[21.48, 14.668, 4.974]
[22.041, 14.866, 3.569]
[21.808, 13.861, 2.734]
[22.263, 13.862, 1.355]
[21.085, 14.233, 0.446]

julia&gt; ChainedBonds(backbone)
ChainedBonds{Float32, Vector{Float32}} with 659 bonds, 658 angles, and 657 dihedrals
Expand All @@ -21,7 +29,15 @@
julia&gt; import Zygote # unlock the `idealize` method for backbones

julia&gt; idealize(backbone, Float32[1.46, 1.52, 1.33], Float32[1.94, 2.04, 2.13])
3×660 Backbone{Float32, Matrix{Float32}}:
22.3486 22.9058 23.2161 24.2046 24.5295 … 23.7832 24.2534 23.9791 24.3124 23.1496
17.5824 17.9775 16.7622 16.8852 15.827 14.3215 14.1375 12.9715 12.7012 13.0422
23.2899 21.9995 21.1408 20.2595 19.3075 9.99834 8.56466 7.98674 6.59122 5.67358</code></pre><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-1"><a class="tag is-link" href="#citeref-1">1</a>In some contexts, the term <em>backbone</em> may be used more loosely, and allow for atoms that are not part of the main continuous chain of atoms. This package does not support storing e.g. oxygen and beta-carbon atoms in the matrix of coordinates, as they are not part of the continuous chain of atoms.</li></ul></section></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="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 1.4.1 on <span class="colophon-date" title="Tuesday 4 June 2024 10:51">Tuesday 4 June 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
660-element Backbone{Float32, Matrix{Float32}}:
[22.348574, 17.582397, 23.289886]
[22.90583, 17.977451, 21.999538]
[23.216103, 16.762234, 21.140835]
[24.204561, 16.88515, 20.259508]
[24.52946, 15.827013, 19.307465]
⋮
[21.501173, 14.705252, 4.9825864]
[22.007494, 14.864742, 3.5582967]
[21.822643, 13.836198, 2.7356021]
[22.24875, 13.874594, 1.3396943]
[21.091076, 14.233609, 0.42247167]</code></pre><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-1"><a class="tag is-link" href="#citeref-1">1</a>In some contexts, the term <em>backbone</em> may be used more loosely, and allow for atoms that are not part of the main continuous chain of atoms. This package does not support storing e.g. oxygen and beta-carbon atoms in the matrix of coordinates, as they are not part of the continuous chain of atoms.</li></ul></section></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="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 1.4.1 on <span class="colophon-date" title="Tuesday 4 June 2024 10:53">Tuesday 4 June 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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