build based on 514f46e

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-08T12:42:03","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-08T13:17:37","documenter_version":"1.5.0"}}

dev/auxiliary/index.html

@@ -15,7 +15,7 @@
 2-element Vector{String}:
  "Serine"
  "Alanine"
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/getseq.jl#L1-L28">source</a></section></article><p>To obtain a list of the residue names of the protein with three- and one-letter codes, use</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/getseq.jl#L1-L28">source</a></section></article><p>To obtain a list of the residue names of the protein with three- and one-letter codes, use</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
 
 julia&gt; getseq(PDBTools.SMALLPDB)
 3-element Vector{String}:
@@ -68,7 +68,7 @@
 
 julia&gt; distance(coor(ligand),protein)
 2.7775834820937417
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/distance.jl#L1-L28">source</a></section></article><p>The distance between atoms, or sets of atoms, can be computed with the <code>distance</code> function. This function returns the <em>minimum distance</em> between the atoms of the sets involved. For example:</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/distance.jl#L1-L28">source</a></section></article><p>The distance between atoms, or sets of atoms, can be computed with the <code>distance</code> function. This function returns the <em>minimum distance</em> between the atoms of the sets involved. For example:</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
 
 julia&gt; model = wget(&quot;1BSX&quot;);
 
@@ -136,7 +136,7 @@
  [45.823, 80.796, 69.974]
  [47.147, 82.98, 71.413]
  [46.541, 82.639, 72.662]
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/coor.jl#L1-L55">source</a></section></article><p>Use the <code>coor</code> function:</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/coor.jl#L1-L55">source</a></section></article><p>Use the <code>coor</code> function:</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
 
 julia&gt; atoms = readPDB(PDBTools.SMALLPDB);
 
@@ -164,7 +164,7 @@
  Minimum atom coordinates: xmin = [-29.301, 57.178, 45.668]
  Maximum atom coordinates: xmax = [47.147, 99.383, 86.886]
  Length in each direction: xlength = [76.448, 42.205, 41.217999999999996]
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/maxmin.jl#L10-L28">source</a></section></article><p>Use <code>maxmin(atoms)</code>, or <code>maxmin(atoms,&quot;resname CA&quot;)</code>, for example:</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/maxmin.jl#L10-L28">source</a></section></article><p>Use <code>maxmin(atoms)</code>, or <code>maxmin(atoms,&quot;resname CA&quot;)</code>, for example:</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
 
 julia&gt; atoms = readPDB(PDBTools.SMALLPDB);
 
@@ -188,7 +188,7 @@
 (1:50:201, [&quot;S225&quot;, &quot;Q275&quot;, &quot;L325&quot;, &quot;L375&quot;, &quot;L425&quot;])
 
 julia&gt; residue_ticks(collect(eachresidue(atoms)); stride=50) # Vector{Residue} as input
-(1:50:201, [&quot;S225&quot;, &quot;Q275&quot;, &quot;L325&quot;, &quot;L375&quot;, &quot;L425&quot;])</code></pre><p>The resulting tuple of residue numbers and labels can be used as <code>xticks</code> in <code>Plots.plot</code>, for example.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/Residue.jl#L299-L340">source</a></section></article><p>The <code>residue_ticks</code> function provides a practical way to define tick labels in plots associated to an amino-acid sequence:</p><pre><code class="language-julia hljs">residue_ticks(
+(1:50:201, [&quot;S225&quot;, &quot;Q275&quot;, &quot;L325&quot;, &quot;L375&quot;, &quot;L425&quot;])</code></pre><p>The resulting tuple of residue numbers and labels can be used as <code>xticks</code> in <code>Plots.plot</code>, for example.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/Residue.jl#L299-L340">source</a></section></article><p>The <code>residue_ticks</code> function provides a practical way to define tick labels in plots associated to an amino-acid sequence:</p><pre><code class="language-julia hljs">residue_ticks(
     atoms (or) residues (or) residue iterator; 
     first=nothing, last=nothing, stride=1, oneletter=true, serial=false,
 )</code></pre><p>The input structure can be provided as a vector of atoms (type <code>Vector{Atom}</code>) a residue iterator (obtained by <code>eachresidue(atoms)</code>) or a vector of residues (obtained by <code>collect(eachresidue(atoms))</code>). </p><p>The function returns a tuple with residue numbers and residue names for the given atoms, to be used as tick labels in plots.</p><p><code>first</code> and <code>last</code> optional keyword parameters are integers that refer to the residue numbers to be included.  The <code>stride</code> option can be used to skip residues and declutter the tick labels.</p><p>If <code>oneletter</code> is <code>false</code>, three-letter residue codes are returned. Residues with unknown names will be  named <code>X</code> or <code>XXX</code>. </p><p>if <code>serial=false</code> the positions of the ticks will be returned as a the serial residue index in the structure. If <code>serial=true</code> the positions of the ticks are returned as their residue numbers. This difference is important if the residue numbers do not start at <code>1</code> and depending on the indexing of the data to be plotted.  </p><div class="admonition is-compat"><header class="admonition-header">Compat</header><div class="admonition-body"><p>The functionality of the <code>residue_ticks</code> as described requires PDBTools version 1.6.0 or greater. </p><p>The <code>serial</code> option was introduced in v1.8.1</p></div></div><h3 id="Example"><a class="docs-heading-anchor" href="#Example">Example</a><a id="Example-1"></a><a class="docs-heading-anchor-permalink" href="#Example" title="Permalink"></a></h3><p>Here we illustrate how to plot the average temperature factor of each residue of a crystallographic model as function of the residues.</p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools, Plots
@@ -210,4 +210,4 @@
 ([1, 11, 21, 31, 41, 51, 61, 71], [&quot;M1&quot;, &quot;K11&quot;, &quot;D21&quot;, &quot;Q31&quot;, &quot;Q41&quot;, &quot;E51&quot;, &quot;I61&quot;, &quot;L71&quot;])
 
 julia&gt; residue_ticks(collect(eachresidue(atoms)); stride=10)
-([1, 11, 21, 31, 41, 51, 61, 71], [&quot;M1&quot;, &quot;K11&quot;, &quot;D21&quot;, &quot;Q31&quot;, &quot;Q41&quot;, &quot;E51&quot;, &quot;I61&quot;, &quot;L71&quot;])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../elements/">« Element properties</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 12:42">Monday 8 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><div data-docstringscollapsed="true"></div></html>
+([1, 11, 21, 31, 41, 51, 61, 71], [&quot;M1&quot;, &quot;K11&quot;, &quot;D21&quot;, &quot;Q31&quot;, &quot;Q41&quot;, &quot;E51&quot;, &quot;I61&quot;, &quot;L71&quot;])</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../elements/">« Element properties</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 13:17">Monday 8 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><div data-docstringscollapsed="true"></div></html>

dev/elements/index.html

@@ -68,7 +68,7 @@
 julia> mass(atoms)
 26.017699999999998
 
-julia&gt; remove_custom_elements!(); </code></pre><p>Here we repeteadly call <code>remove_custom_elements!()</code> to guarantee the proper execution of the test codes, without any custom elements predefined.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/elements.jl#L117-L155">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="PDBTools.remove_custom_elements!" href="#PDBTools.remove_custom_elements!"><code>PDBTools.remove_custom_elements!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">remove_custom_elements!()</code></pre><p>Remove all custom elements from the elements dictionary.</p><p><strong>Example</strong></p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
+julia&gt; remove_custom_elements!(); </code></pre><p>Here we repeteadly call <code>remove_custom_elements!()</code> to guarantee the proper execution of the test codes, without any custom elements predefined.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/elements.jl#L117-L155">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="PDBTools.remove_custom_elements!" href="#PDBTools.remove_custom_elements!"><code>PDBTools.remove_custom_elements!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">remove_custom_elements!()</code></pre><p>Remove all custom elements from the elements dictionary.</p><p><strong>Example</strong></p><pre><code class="language-julia-repl hljs">julia&gt; using PDBTools
 
 julia&gt; remove_custom_elements!();
 
@@ -81,4 +81,4 @@
 julia&gt; remove_custom_elements!();
 
 julia&gt; element(Atom(name=&quot;GN&quot;)) # returns `nothing`
-</code></pre><p>Here we repeteadly call <code>remove_custom_elements!()</code> to guarantee the proper execution of the test codes, without any custom elements predefined.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/c7ec395a47b21f5a2a2a73b5cb541db8d9ad7fe6/src/elements.jl#L175-L202">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../selections/">« Selections</a><a class="docs-footer-nextpage" href="../auxiliary/">Auxiliary functions »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 12:42">Monday 8 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>Here we repeteadly call <code>remove_custom_elements!()</code> to guarantee the proper execution of the test codes, without any custom elements predefined.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/PDBTools.jl/blob/514f46eb04d315610c31cf0e9ad3cacd56ca8f70/src/elements.jl#L175-L202">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../selections/">« Selections</a><a class="docs-footer-nextpage" href="../auxiliary/">Auxiliary functions »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 13:17">Monday 8 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/index.html

@@ -46,4 +46,4 @@
  0.17811534472805368
  ⋮
  0.8254040639975442
- 0.6153943592336552</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../auxiliary/">« Auxiliary functions</a><a class="docs-footer-nextpage" href="../tools/">Tools »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 12:42">Monday 8 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ 0.6153943592336552</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../auxiliary/">« Auxiliary functions</a><a class="docs-footer-nextpage" href="../tools/">Tools »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 8 July 2024 13:17">Monday 8 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>