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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>File IO · MDToolbox.jl</title><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/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="../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">MDToolbox.jl</span></div><form class="docs-search" action="../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">MDToolbox.jl</a></li><li><a class="tocitem" href="../installation/">Installation</a></li><li><span class="tocitem">Getting started</span><ul><li><a class="tocitem" href="../getting_started01/">Input and Output</a></li><li><a class="tocitem" href="../getting_started02/">TrjArray type</a></li><li><a class="tocitem" href="../getting_started03/">Atom selection</a></li></ul></li><li><span class="tocitem">Examples</span><ul><li><a class="tocitem" href="../superimpose_rmsd/">Superimpose and RMSD</a></li><li><a class="tocitem" href="../free_energy_surface/">Free energy surface from MD data</a></li><li><a class="tocitem" href="../wham_example/">WHAM (Weighted Histogram Analysis Method)</a></li></ul></li><li><span class="tocitem">References</span><ul><li class="is-active"><a class="tocitem" href>File IO</a></li><li><a class="tocitem" href="../structure/">Structural computations</a></li><li><a class="tocitem" href="../reduction/">Reductions</a></li><li><a class="tocitem" href="../wham/">WHAM (Weighted Histogram Analysis Method)</a></li><li><a class="tocitem" href="../mbar/">MBAR (Multistate Bennett acceptance ratio)</a></li><li><a class="tocitem" href="../msm/">Makorv state models</a></li></ul></li><li><a class="tocitem" href="../workflow_for_developers/">Workflow for developers</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"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">References</a></li><li class="is-active"><a href>File IO</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>File IO</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/matsunagalab/MDToolbox.jl/blob/master/docs/src/fileio.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="File-IO"><a class="docs-heading-anchor" href="#File-IO">File IO</a><a id="File-IO-1"></a><a class="docs-heading-anchor-permalink" href="#File-IO" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="MDToolbox.mdload-Tuple{AbstractString}" href="#MDToolbox.mdload-Tuple{AbstractString}"><code>MDToolbox.mdload</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">mdload(filename::AbstractString; index=nothing, top::TrjArray=nothing) -> ta::TrjArray</code></pre><p>Function for reading bimolecular structure files or molecular dynamics trajectories. This function automatically detects files types from the filename extension of input <code>filename</code>. Currently, PDB, PSF, DCD, NetCDF, and namdbin(namd restart file) formats are available. For reading subset atoms from the trajectory files, the user can specify atom indices as <code>index::AbstractVector{Int}</code>. Returns a TrjArray variable <code>ta</code>.</p><p>If the user wants to attach a topology information read from PSF, PDB, or other files to MD trajectory, the user can give an addtional option <code>top=ta:TrjArray</code>. If the option is given the topology information is applied.</p><p><strong>Example</strong></p><pre><code class="language-julia-repl">julia> ta = mdload("1ake.psf") | ||
| julia> ta = mdload("1ake.dcd", top=ta)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/matsunagalab/MDToolbox.jl/blob/449a6e0e246e98dc57d53be62ca3bef943ac4489/src/fileio.jl#L1-L18">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="MDToolbox.mdsave-Tuple{AbstractString, TrjArray}" href="#MDToolbox.mdsave-Tuple{AbstractString, TrjArray}"><code>MDToolbox.mdsave</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">mdsave(filename::AbstractString, ta::TrjArray)</code></pre><p>Function for writing bimolecular structure files or molecular dynamics trajectories. This function automatically detects files types from the filename extension of input <code>filename</code>. Currently, PDB, PSF, NetCDF, and namdbin(namd restart file) formats are available.</p><p><strong>Example</strong></p><pre><code class="language-julia-repl">julia> ta = TrjArray(xyz=randn(100, 9)) | ||
| julia> ta = mdsave("1ake.nc", ta)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/matsunagalab/MDToolbox.jl/blob/449a6e0e246e98dc57d53be62ca3bef943ac4489/src/fileio.jl#L45-L57">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../wham_example/">« WHAM (Weighted Histogram Analysis Method)</a><a class="docs-footer-nextpage" href="../structure/">Structural computations »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Friday 1 March 2024 15:56">Friday 1 March 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> | ||
| julia> ta = mdload("1ake.dcd", top=ta)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/matsunagalab/MDToolbox.jl/blob/3250c6617ab0f226df1c528d92cda49e408f1c03/src/fileio.jl#L1-L18">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="MDToolbox.mdsave-Tuple{AbstractString, TrjArray}" href="#MDToolbox.mdsave-Tuple{AbstractString, TrjArray}"><code>MDToolbox.mdsave</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">mdsave(filename::AbstractString, ta::TrjArray)</code></pre><p>Function for writing bimolecular structure files or molecular dynamics trajectories. This function automatically detects files types from the filename extension of input <code>filename</code>. Currently, PDB, PSF, NetCDF, and namdbin(namd restart file) formats are available.</p><p><strong>Example</strong></p><pre><code class="language-julia-repl">julia> ta = TrjArray(xyz=randn(100, 9)) | ||
| julia> ta = mdsave("1ake.nc", ta)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/matsunagalab/MDToolbox.jl/blob/3250c6617ab0f226df1c528d92cda49e408f1c03/src/fileio.jl#L45-L57">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../wham_example/">« WHAM (Weighted Histogram Analysis Method)</a><a class="docs-footer-nextpage" href="../structure/">Structural computations »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Monday 4 March 2024 09:12">Monday 4 March 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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