build based on 728cc78

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-10-30T04:15:34","documenter_version":"1.1.2"}}
+{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-11-06T04:16:36","documenter_version":"1.1.2"}}

dev/api/index.html

@@ -83,4 +83,4 @@
 waterselector(at)</code></pre><p>Determines if an <code>AbstractResidue</code> or <code>AbstractAtom</code> represents a water molecule, i.e. whether the residue name is in <code>waterresnames</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L1744-L1750">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="BioStructures.writemmcif-Tuple{AbstractString, MMCIFDict}" href="#BioStructures.writemmcif-Tuple{AbstractString, MMCIFDict}"><code>BioStructures.writemmcif</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">writemmcif(output, element, atom_selectors...; gzip=false)
 writemmcif(output, mmcif_dict; gzip=false)</code></pre><p>Write a <code>StructuralElementOrList</code> or a <code>MMCIFDict</code> to a mmCIF format file or output stream.</p><p>Atom selector functions can be given as additional arguments - only atoms that return <code>true</code> from all the functions are retained. The keyword argument <code>expand_disordered</code> (default <code>true</code>) determines whether to return all copies of disordered residues and atoms. The keyword argument <code>gzip</code> (default <code>false</code>) determines if the output is gzipped.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/mmcif.jl#L390-L402">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="BioStructures.writemultimmcif-Tuple{AbstractString, Dict{String, MMCIFDict}}" href="#BioStructures.writemultimmcif-Tuple{AbstractString, Dict{String, MMCIFDict}}"><code>BioStructures.writemultimmcif</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">writemultimmcif(filepath, cifs; gzip=false)
 writemultimmcif(io, cifs; gzip=false)</code></pre><p>Write multiple <code>MMCIFDict</code>s as a <code>Dict{String, MMCIFDict}</code> to a filepath or stream. The keyword argument <code>gzip</code> (default <code>false</code>) determines if the output is gzipped.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/mmcif.jl#L618-L624">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="BioStructures.writepdb-Tuple{AbstractString, StructuralElementOrList, Vararg{Function}}" href="#BioStructures.writepdb-Tuple{AbstractString, StructuralElementOrList, Vararg{Function}}"><code>BioStructures.writepdb</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">writepdb(output, element, atom_selectors...)</code></pre><p>Write a <code>StructuralElementOrList</code> to a Protein Data Bank (PDB) format file or output stream.</p><p>Only ATOM, HETATM, MODEL and ENDMDL records are written - there is no header and there are no TER records. Atom selector functions can be given as additional arguments - only atoms that return <code>true</code> from all the functions are retained. The keyword argument <code>expand_disordered</code> (default <code>true</code>) determines whether to return all copies of disordered residues and atoms.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/pdb.jl#L795-L807">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="BioStructures.x!-Tuple{Atom, Real}" href="#BioStructures.x!-Tuple{Atom, Real}"><code>BioStructures.x!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">x!(at, val)</code></pre><p>Set the x coordinate of an <code>AbstractAtom</code> to <code>val</code>.</p><p>For <code>DisorderedAtom</code>s only the default atom is updated.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L429-L435">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="BioStructures.x-Tuple{Atom}" href="#BioStructures.x-Tuple{Atom}"><code>BioStructures.x</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">x(at)</code></pre><p>Get the x coordinate of an <code>AbstractAtom</code> as a <code>Float64</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L421-L425">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="BioStructures.y!-Tuple{Atom, Real}" href="#BioStructures.y!-Tuple{Atom, Real}"><code>BioStructures.y!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">y!(at, val)</code></pre><p>Set the y coordinate of an <code>AbstractAtom</code> to <code>val</code>.</p><p>For <code>DisorderedAtom</code>s only the default atom is updated.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L447-L453">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="BioStructures.y-Tuple{Atom}" href="#BioStructures.y-Tuple{Atom}"><code>BioStructures.y</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">y(at)</code></pre><p>Get the y coordinate of an <code>AbstractAtom</code> as a <code>Float64</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L439-L443">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="BioStructures.z!-Tuple{Atom, Real}" href="#BioStructures.z!-Tuple{Atom, Real}"><code>BioStructures.z!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">z!(at, val)</code></pre><p>Set the z coordinate of an <code>AbstractAtom</code> to <code>val</code>.</p><p>For <code>DisorderedAtom</code>s only the default atom is updated.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L465-L471">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="BioStructures.z-Tuple{Atom}" href="#BioStructures.z-Tuple{Atom}"><code>BioStructures.z</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">z(at)</code></pre><p>Get the z coordinate of an <code>AbstractAtom</code> as a <code>Float64</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/model.jl#L457-L461">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="MMTF.writemmtf-Tuple{Union{AbstractString, IO}, MMTFDict}" href="#MMTF.writemmtf-Tuple{Union{AbstractString, IO}, MMTFDict}"><code>MMTF.writemmtf</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">writemmtf(output, element, atom_selectors...; gzip=false)
-writemmtf(output, mmtf_dict; gzip=false)</code></pre><p>Write a <code>StructuralElementOrList</code> or a <code>MMTFDict</code> to a MMTF file or output stream.</p><p>Atom selector functions can be given as additional arguments - only atoms that return <code>true</code> from all the functions are retained. The keyword argument <code>expand_disordered</code> (default <code>true</code>) determines whether to return all copies of disordered residues and atoms. The keyword argument <code>gzip</code> (default <code>false</code>) determines if the file should be gzipped.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/mmtf.jl#L219-L232">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" 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="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="Monday 30 October 2023 04:15">Monday 30 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+writemmtf(output, mmtf_dict; gzip=false)</code></pre><p>Write a <code>StructuralElementOrList</code> or a <code>MMTFDict</code> to a MMTF file or output stream.</p><p>Atom selector functions can be given as additional arguments - only atoms that return <code>true</code> from all the functions are retained. The keyword argument <code>expand_disordered</code> (default <code>true</code>) determines whether to return all copies of disordered residues and atoms. The keyword argument <code>gzip</code> (default <code>false</code>) determines if the file should be gzipped.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/728cc78fd7da5cd019efe524c521579d96600c9c/src/mmtf.jl#L219-L232">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" 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="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="Monday 6 November 2023 04:16">Monday 6 November 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/documentation/index.html

@@ -3422,4 +3422,4 @@
 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/christophfeinauer/PdbTool.jl">PdbTool.jl</a> - read and work with PDB 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="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="Monday 30 October 2023 04:15">Monday 30 October 2023</span>. Using Julia version 1.9.3.</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/christophfeinauer/PdbTool.jl">PdbTool.jl</a> - read and work with PDB 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="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="Monday 6 November 2023 04:16">Monday 6 November 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>