build based on 35fc501

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-23T13:41:17","documenter_version":"1.4.0"}}
+{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-05-24T13:40:11","documenter_version":"1.4.0"}}

dev/documentation/index.html

@@ -118,7 +118,7 @@
 read("/path/to/pdb/file.pdb", PDB, run_dssp=true)
 
 # Assign secondary structure using STRIDE
-read(&quot;/path/to/pdb/file.pdb&quot;, PDB, run_strude=true)</code></pre><p><a href="../api/#BioStructures.rundssp!-Tuple{Model}"><code>rundssp!</code></a>, <a href="../api/#BioStructures.runstride!-Tuple{Model}"><code>runstride!</code></a>, <a href="../api/#BioStructures.rundssp-Tuple{Union{Model, ProteinStructure}}"><code>rundssp</code></a> and <a href="../api/#BioStructures.runstride-Tuple{Union{Model, ProteinStructure}}"><code>runstride</code></a> can also be used to assign secondary structure to a <a href="../api/#BioStructures.ProteinStructure"><code>ProteinStructure</code></a> or <a href="../api/#BioStructures.Model"><code>Model</code></a>:</p><pre><code class="language-julia hljs">rundssp!(struc)
+read(&quot;/path/to/pdb/file.pdb&quot;, PDB, run_stride=true)</code></pre><p><a href="../api/#BioStructures.rundssp!-Tuple{Model}"><code>rundssp!</code></a>, <a href="../api/#BioStructures.runstride!-Tuple{Model}"><code>runstride!</code></a>, <a href="../api/#BioStructures.rundssp-Tuple{Union{Model, ProteinStructure}}"><code>rundssp</code></a> and <a href="../api/#BioStructures.runstride-Tuple{Union{Model, ProteinStructure}}"><code>runstride</code></a> can also be used to assign secondary structure to a <a href="../api/#BioStructures.ProteinStructure"><code>ProteinStructure</code></a> or <a href="../api/#BioStructures.Model"><code>Model</code></a>:</p><pre><code class="language-julia hljs">rundssp!(struc)
 runstride!(struc)</code></pre><p>The assignment process may fail if the structure is too large, since we use an intermediate PDB file where the atom serial cannot exceed 99999 and the chain ID must be a single character.</p><p>To get access to the secondary structure code of a residue or atom as a <code>Char</code>:</p><pre><code class="language-julia hljs">sscode(res)
 sscode(at)</code></pre><p>The secondary structure code of a residue can be changed using <a href="../api/#BioStructures.sscode!-Tuple{Residue, Any}"><code>sscode!</code></a>.</p><p><a href="../api/#BioStructures.rundssp-Tuple{Union{Model, ProteinStructure}}"><code>rundssp</code></a> and <a href="../api/#BioStructures.runstride-Tuple{Union{Model, ProteinStructure}}"><code>runstride</code></a> can also be run directly on structure files:</p><pre><code class="language-julia hljs">rundssp(&quot;/path/to/pdb/file.pdb&quot;, &quot;out.dssp&quot;) # Also works with mmCIF files
 runstride(&quot;/path/to/pdb/file.pdb&quot;, &quot;out.stride&quot;)</code></pre><p>See the documentation for <a href="https://docs.juliahub.com/General/DSSP_jll/stable/autodocs">DSSP_jll</a> and <a href="https://docs.juliahub.com/General/STRIDE_jll/stable/autodocs">STRIDE_jll</a>, and also <a href="https://github.com/m3g/ProteinSecondaryStructures.jl">ProteinSecondaryStructures.jl</a>, for other ways to run these programs.</p><h2 id="Downloading-PDB-files"><a class="docs-heading-anchor" href="#Downloading-PDB-files">Downloading PDB files</a><a id="Downloading-PDB-files-1"></a><a class="docs-heading-anchor-permalink" href="#Downloading-PDB-files" title="Permalink"></a></h2><p>To download a PDB file to a specified directory:</p><pre><code class="language-julia hljs">downloadpdb(&quot;1EN2&quot;, dir=&quot;path/to/pdb/directory&quot;)</code></pre><p>To download multiple PDB files to a specified directory:</p><pre><code class="language-julia hljs">downloadpdb([&quot;1EN2&quot;, &quot;1ALW&quot;, &quot;1AKE&quot;], dir=&quot;path/to/pdb/directory&quot;)</code></pre><p>To download a PDB file in PDB, XML, mmCIF or MMTF format use the <code>format</code> argument:</p><pre><code class="language-julia hljs"># To get mmCIF
@@ -3424,4 +3424,4 @@
 var viewer = $3Dmol.viewers['3dmol_viewer_2'];
 viewer.render();
 });
-</script><p>See the <a href="http://nbviewer.jupyter.org/github/jgreener64/Bio3DView.jl/blob/master/examples/tutorial.ipynb">Bio3DView.jl tutorial</a> for more information. <a href="https://github.com/BioJulia/BioMakie.jl">BioMakie.jl</a> can also be used to visualise BioStructures objects.</p><h2 id="Related-software"><a class="docs-heading-anchor" href="#Related-software">Related software</a><a id="Related-software-1"></a><a class="docs-heading-anchor-permalink" href="#Related-software" title="Permalink"></a></h2><p>Other packages in the Julia ecosystem that deal with structural bioinformatics or related fields include:</p><ul><li><a href="https://github.com/diegozea/MIToS.jl">MIToS.jl</a> - protein sequence and structure analysis.</li><li><a href="https://github.com/m3g/PDBTools.jl">PDBTools.jl</a> - read and write PDB files.</li><li><a href="https://github.com/christophfeinauer/PdbTool.jl">PdbTool.jl</a> - read and work with PDB files.</li><li><a href="https://github.com/chemfiles/Chemfiles.jl">Chemfiles.jl</a> - read and write various chemistry trajectory files.</li><li><a href="https://github.com/jgreener64/Bio3DView.jl">Bio3DView.jl</a> - view molecular structures (see <a href="#Visualising-structures">Visualising structures</a>).</li><li><a href="https://github.com/BioJulia/BioMakie.jl">BioMakie.jl</a> - view molecular structures and sequence alignments.</li><li><a href="https://github.com/m3g/ProteinSecondaryStructures.jl">ProteinSecondaryStructures.jl</a> - parses DSSP and STRIDE outputs.</li><li><a href="https://github.com/BioJulia/MMTF.jl">MMTF.jl</a> - read and write MMTF files. BioStructures.jl builds on top of MMTF.jl.</li><li><a href="https://github.com/jgreener64/ProteinEnsembles.jl">ProteinEnsembles.jl</a> - model ensembles of protein structures.</li><li><a href="https://github.com/jgreener64/Molly.jl">Molly.jl</a> - molecular dynamics of biomolecules.</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../examples/">Examples »</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 1.4.0 on <span class="colophon-date" title="Thursday 23 May 2024 13:41">Thursday 23 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</script><p>See the <a href="http://nbviewer.jupyter.org/github/jgreener64/Bio3DView.jl/blob/master/examples/tutorial.ipynb">Bio3DView.jl tutorial</a> for more information. <a href="https://github.com/BioJulia/BioMakie.jl">BioMakie.jl</a> can also be used to visualise BioStructures objects.</p><h2 id="Related-software"><a class="docs-heading-anchor" href="#Related-software">Related software</a><a id="Related-software-1"></a><a class="docs-heading-anchor-permalink" href="#Related-software" title="Permalink"></a></h2><p>Other packages in the Julia ecosystem that deal with structural bioinformatics or related fields include:</p><ul><li><a href="https://github.com/diegozea/MIToS.jl">MIToS.jl</a> - protein sequence and structure analysis.</li><li><a href="https://github.com/m3g/PDBTools.jl">PDBTools.jl</a> - read and write PDB files.</li><li><a href="https://github.com/christophfeinauer/PdbTool.jl">PdbTool.jl</a> - read and work with PDB files.</li><li><a href="https://github.com/chemfiles/Chemfiles.jl">Chemfiles.jl</a> - read and write various chemistry trajectory files.</li><li><a href="https://github.com/jgreener64/Bio3DView.jl">Bio3DView.jl</a> - view molecular structures (see <a href="#Visualising-structures">Visualising structures</a>).</li><li><a href="https://github.com/BioJulia/BioMakie.jl">BioMakie.jl</a> - view molecular structures and sequence alignments.</li><li><a href="https://github.com/m3g/ProteinSecondaryStructures.jl">ProteinSecondaryStructures.jl</a> - parses DSSP and STRIDE outputs.</li><li><a href="https://github.com/BioJulia/MMTF.jl">MMTF.jl</a> - read and write MMTF files. BioStructures.jl builds on top of MMTF.jl.</li><li><a href="https://github.com/jgreener64/ProteinEnsembles.jl">ProteinEnsembles.jl</a> - model ensembles of protein structures.</li><li><a href="https://github.com/jgreener64/Molly.jl">Molly.jl</a> - molecular dynamics of biomolecules.</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../examples/">Examples »</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 1.4.0 on <span class="colophon-date" title="Friday 24 May 2024 13:40">Friday 24 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/index.html

@@ -73,4 +73,4 @@
 describe(df) # Show summary
 mean(df.tempfactor) # Column-wise operations
 sort(df, :x) # Sorting
-CSV.write(&quot;1ALW.csv&quot;, df) # CSV file writing</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../documentation/">« Documentation</a><a class="docs-footer-nextpage" href="../api/">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 1.4.0 on <span class="colophon-date" title="Thursday 23 May 2024 13:41">Thursday 23 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+CSV.write(&quot;1ALW.csv&quot;, df) # CSV file writing</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../documentation/">« Documentation</a><a class="docs-footer-nextpage" href="../api/">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 1.4.0 on <span class="colophon-date" title="Friday 24 May 2024 13:40">Friday 24 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>