-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Documenter.jl
committed
Mar 1, 2024
1 parent
f1ec032
commit e57a304
Showing
16 changed files
with
47 additions
and
47 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| <!DOCTYPE html> | ||
| <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/9aa5c0967c7b75a344e132057da177c767ebd05c/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/9aa5c0967c7b75a344e132057da177c767ebd05c/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 24 November 2023 06:02">Friday 24 November 2023</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/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> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.