build based on b716d64

Author: Documenter.jl

dev/.documenter-siteinfo.json

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-{"documenter":{"julia_version":"1.12.2","generation_timestamp":"2025-12-01T04:46:35","documenter_version":"1.16.1"}}
+{"documenter":{"julia_version":"1.12.2","generation_timestamp":"2025-12-08T04:30:26","documenter_version":"1.16.1"}}

dev/api/index.html

@@ -92,4 +92,4 @@
 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/select.jl#L352-L358">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.writemmcif-Tuple{AbstractString, MMCIFDict}"><a class="docstring-binding" href="#BioStructures.writemmcif-Tuple{AbstractString, MMCIFDict}"><code>BioStructures.writemmcif</code></a> — <span class="docstring-category">Method</span></summary><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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/mmcif.jl#L458-L470">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.writemmtf"><a class="docstring-binding" href="#BioStructures.writemmtf"><code>BioStructures.writemmtf</code></a> — <span class="docstring-category">Function</span></summary><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>Requires the MMTF.jl package to be imported. 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L1827-L1841">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.writemultimmcif-Tuple{AbstractString, Dict{String, MMCIFDict}}"><a class="docstring-binding" href="#BioStructures.writemultimmcif-Tuple{AbstractString, Dict{String, MMCIFDict}}"><code>BioStructures.writemultimmcif</code></a> — <span class="docstring-category">Method</span></summary><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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/mmcif.jl#L686-L692">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.writepdb-Tuple{AbstractString, StructuralElementOrList, Vararg{Function}}"><a class="docstring-binding" href="#BioStructures.writepdb-Tuple{AbstractString, StructuralElementOrList, Vararg{Function}}"><code>BioStructures.writepdb</code></a> — <span class="docstring-category">Method</span></summary><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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/pdb.jl#L349-L361">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.@sel_str-Tuple{Any}"><a class="docstring-binding" href="#BioStructures.@sel_str-Tuple{Any}"><code>BioStructures.@sel_str</code></a> — <span class="docstring-category">Macro</span></summary><section><div><p>String selection syntax.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/select.jl#L457">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.x"><a class="docstring-binding" href="#BioStructures.x"><code>BioStructures.x</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">x(at)</code></pre><p>Get the x coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L472-L476">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.x!"><a class="docstring-binding" href="#BioStructures.x!"><code>BioStructures.x!</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">x!(at, val)</code></pre><p>Set the x coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L480-L486">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.y"><a class="docstring-binding" href="#BioStructures.y"><code>BioStructures.y</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">y(at)</code></pre><p>Get the y coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L490-L494">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.y!"><a class="docstring-binding" href="#BioStructures.y!"><code>BioStructures.y!</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">y!(at, val)</code></pre><p>Set the y coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L498-L504">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.z"><a class="docstring-binding" href="#BioStructures.z"><code>BioStructures.z</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">z(at)</code></pre><p>Get the z coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L508-L512">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.z!"><a class="docstring-binding" href="#BioStructures.z!"><code>BioStructures.z!</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">z!(at, val)</code></pre><p>Set the z coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L516-L522">source</a></section></details></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 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Using Julia version 1.12.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/mmcif.jl#L686-L692">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.writepdb-Tuple{AbstractString, StructuralElementOrList, Vararg{Function}}"><a class="docstring-binding" href="#BioStructures.writepdb-Tuple{AbstractString, StructuralElementOrList, Vararg{Function}}"><code>BioStructures.writepdb</code></a> — <span class="docstring-category">Method</span></summary><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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/pdb.jl#L349-L361">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.@sel_str-Tuple{Any}"><a class="docstring-binding" href="#BioStructures.@sel_str-Tuple{Any}"><code>BioStructures.@sel_str</code></a> — <span class="docstring-category">Macro</span></summary><section><div><p>String selection syntax.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/BioStructures.jl/blob/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/select.jl#L457">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.x"><a class="docstring-binding" href="#BioStructures.x"><code>BioStructures.x</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">x(at)</code></pre><p>Get the x coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L472-L476">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.x!"><a class="docstring-binding" href="#BioStructures.x!"><code>BioStructures.x!</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">x!(at, val)</code></pre><p>Set the x coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L480-L486">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.y"><a class="docstring-binding" href="#BioStructures.y"><code>BioStructures.y</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">y(at)</code></pre><p>Get the y coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L490-L494">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.y!"><a class="docstring-binding" href="#BioStructures.y!"><code>BioStructures.y!</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">y!(at, val)</code></pre><p>Set the y coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L498-L504">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.z"><a class="docstring-binding" href="#BioStructures.z"><code>BioStructures.z</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">z(at)</code></pre><p>Get the z coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L508-L512">source</a></section></details></article><article><details class="docstring" open="true"><summary id="BioStructures.z!"><a class="docstring-binding" href="#BioStructures.z!"><code>BioStructures.z!</code></a> — <span class="docstring-category">Function</span></summary><section><div><pre><code class="language-julia hljs">z!(at, val)</code></pre><p>Set the z coordinate in Å 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/b716d643e6fd6dc7c520cfaaa6d0b9d5704eca6c/src/model.jl#L516-L522">source</a></section></details></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 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Using Julia version 1.12.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>