build based on 52d240d

dev/faq/index.html

@@ -34,4 +34,4 @@
 julia> typeof(genome_allnodes)
 TopologicalGenome</code></pre><p>In case where all clusterings lead to the same genome, it can simply be accessed by calling <code>first(topo)</code>.</p><p>Having obtained a <a href="../lib/public/#CrystalNets.TopologicalGenome"><code>TopologicalGenome</code></a>, the topological genome itself can accessed by converting it to a <code>PeriodicGraph</code>:</p><pre><code class="language-julia-repl hljs">julia&gt; genome = PeriodicGraph(genome_allnodes)
 PeriodicGraph3D(6, PeriodicEdge3D[(1, 2, (0,0,0)), (1, 3, (0,0,0)), (1, 4, (0,0,0)), (1, 4, (0,0,1)), (1, 5, (0,0,0)), (1, 6, (0,0,0)), (2, 4, (0,0,1)), (2, 6, (-1,0,0)), (3, 4, (0,0,1)), (3, 5, (0,-1,0)), (4, 5, (0,0,0)), (4, 6, (0,0,0))])</code></pre><p>In case of error during topology identification, the returned <code>genome</code> is a <code>PeriodicGraph{0}</code>.</p><p>The string representation of the genome is simply <code>string(genome)</code>:</p><pre><code class="language-im19faq hljs">julia&gt; string(genome)
-&quot;3 1 2 0 0 0 1 3 0 0 0 1 4 0 0 0 1 4 0 0 1 1 5 0 0 0 1 6 0 0 0 2 4 0 0 1 2 6 -1 0 0 3 4 0 0 1 3 5 0 -1 0 4 5 0 0 0 4 6 0 0 0&quot;</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../python/">« Python</a><a class="docs-footer-nextpage" href="../lib/public/">Public »</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> version 0.27.25 on <span class="colophon-date" title="Monday 13 May 2024 15:18">Monday 13 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+&quot;3 1 2 0 0 0 1 3 0 0 0 1 4 0 0 0 1 4 0 0 1 1 5 0 0 0 1 6 0 0 0 2 4 0 0 1 2 6 -1 0 0 3 4 0 0 1 3 5 0 -1 0 4 5 0 0 0 4 6 0 0 0&quot;</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../python/">« Python</a><a class="docs-footer-nextpage" href="../lib/public/">Public »</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> version 0.27.25 on <span class="colophon-date" title="Monday 13 May 2024 15:48">Monday 13 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -25,4 +25,4 @@
 create_app(root, INSTALLATION_PATH;
            precompile_statements_file=abspath(root, "src", "precompile_statements.jl"),
            filter_stdlibs=true)</code></pre><p>Compilation can take between fifteen minutes and an hour, depending on your hardware and the version of Julia.</p><p>The executable will be located in the &quot;bin&quot; subdirectory of the specified <code>INSTALLATION_PATH</code>, under the name &quot;CrystalNets&quot;.</p><p>The executable can then simply be used on a chemical file:</p><pre><code class="language-bash hljs">$ CrystalNets /path/to/diamond.cif
-dia</code></pre><p>Run <code>CrystalNets --help</code> for the list of options available to the executable.</p><div class="admonition is-success"><header class="admonition-header">Tip</header><div class="admonition-body"><p>In terms of performance, the compiled executable is the best option if you only want to identify a few structures from time to time. Using <a href="https://progs.coudert.name/topology">the website</a> is recommended as well for this use-case, unless the nets you study are too big.</p><p>For intensive workloads with many structures to identify, it is best to use <code>CrystalNets.jl</code> as a Julia module through the <a href="lib/public/#CrystalNets.determine_topology_dataset"><code>determine_topology_dataset</code></a> function. The module is also the best option to perform more advanced analyses on the net in Julia, or to use the <a href="lib/public/#CrystalNets.Options"><code>Options</code></a> unavailable to the executable.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="visualization/">Visualization »</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> version 0.27.25 on <span class="colophon-date" title="Monday 13 May 2024 15:18">Monday 13 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+dia</code></pre><p>Run <code>CrystalNets --help</code> for the list of options available to the executable.</p><div class="admonition is-success"><header class="admonition-header">Tip</header><div class="admonition-body"><p>In terms of performance, the compiled executable is the best option if you only want to identify a few structures from time to time. Using <a href="https://progs.coudert.name/topology">the website</a> is recommended as well for this use-case, unless the nets you study are too big.</p><p>For intensive workloads with many structures to identify, it is best to use <code>CrystalNets.jl</code> as a Julia module through the <a href="lib/public/#CrystalNets.determine_topology_dataset"><code>determine_topology_dataset</code></a> function. The module is also the best option to perform more advanced analyses on the net in Julia, or to use the <a href="lib/public/#CrystalNets.Options"><code>Options</code></a> unavailable to the executable.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="visualization/">Visualization »</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> version 0.27.25 on <span class="colophon-date" title="Monday 13 May 2024 15:48">Monday 13 May 2024</span>. Using Julia version 1.10.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>