build based on 4c39448

dev/contrib/index.html

@@ -47,4 +47,4 @@
 neutral_contributions = contributions(solute,R.solute_atom,neutral_residues)</code></pre><p>The <code>charged</code> and <code>neutral</code> outputs are vectors containing the contributions of these residues to the total MDDF. The corresponding plot is:   </p><pre><code class="language-julia hljs">plot(results.d,results.mddf,label=&quot;Total MDDF&quot;,linewidth=2)
 plot!(results.d,charged_contributions,label=&quot;Charged residues&quot;,linewidth=2)
 plot!(results.d,neutral_contributions,label=&quot;Neutral residues&quot;,linewidth=2)
-plot!(xlabel=&quot;Distance / Å&quot;,ylabel=&quot;MDDF&quot;)</code></pre><p>Resulting in:</p><img src="../figures/charged_and_neutral.png" width="60%"><p>Note here how charged residues contribute strongly to the peak at hydrogen-bonding distances, but much less in general. Of course all selection options could be used, to obtain the contributions of specific types of residues, atoms, the backbone, the side-chains, etc. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../results/">« Results</a><a class="docs-footer-nextpage" href="../save/">Save and load »</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 7 August 2023 01:21">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot!(xlabel=&quot;Distance / Å&quot;,ylabel=&quot;MDDF&quot;)</code></pre><p>Resulting in:</p><img src="../figures/charged_and_neutral.png" width="60%"><p>Note here how charged residues contribute strongly to the peak at hydrogen-bonding distances, but much less in general. Of course all selection options could be used, to obtain the contributions of specific types of residues, atoms, the backbone, the side-chains, etc. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../results/">« Results</a><a class="docs-footer-nextpage" href="../save/">Save and load »</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 7 August 2023 01:29">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/examples/index.html

@@ -68,4 +68,4 @@
     output_file="grid.pdb",
     dmin=1.5,
     dmax=3.5
-)</code></pre><p>The command above will generate the grid, save it to <code>grid.pdb</code> and let it available in the <code>grid.pdb</code> array of atoms, for further inspection, if desired. </p><p>By changing <code>dmin</code>, <code>dmax</code>, and <code>step</code>, one controls the grid size and resolution. This may generate very large output files.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../quickguide/">« Quick Guide</a><a class="docs-footer-nextpage" href="../selection/">Set solute and solvent »</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 7 August 2023 01:21">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+)</code></pre><p>The command above will generate the grid, save it to <code>grid.pdb</code> and let it available in the <code>grid.pdb</code> array of atoms, for further inspection, if desired. </p><p>By changing <code>dmin</code>, <code>dmax</code>, and <code>step</code>, one controls the grid size and resolution. This may generate very large output files.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../quickguide/">« Quick Guide</a><a class="docs-footer-nextpage" href="../selection/">Set solute and solvent »</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 7 August 2023 01:29">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -16,4 +16,4 @@
 <img width="50%" src="./figures/Gamma.png">
 <br>
 <b>Preferential interaction parameters obtained for the solvation of a protein by ionic liquids.</b><br><br>
-</center><p>In particular, the plot shows that besides being preferentially excluded from the protein surface at high concentrations in the native state, suggesting protein folding stabilization, the interactions with the protein in the denatured states are stronger, leading to denaturation at all concentrations. </p><h2 id="References"><a class="docs-heading-anchor" href="#References">References</a><a id="References-1"></a><a class="docs-heading-anchor-permalink" href="#References" title="Permalink"></a></h2><ul><li><p>L. Martínez, <strong>ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective.</strong> <em>J. Mol. Liq.</em> 347, 117945, 2022. <a href="https://doi.org/10.1016/j.molliq.2021.117945">[Full Text]</a></p></li><li><p>L. Martínez, S. Shimizu, <strong>Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions.</strong> <em>J. Chem. Theor.  Comp.</em> 13, 6358–6372, 2017. <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00599">[Full Text]</a></p></li></ul><h2 id="See-also"><a class="docs-heading-anchor" href="#See-also">See also</a><a id="See-also-1"></a><a class="docs-heading-anchor-permalink" href="#See-also" title="Permalink"></a></h2><h3 id="Seminar"><a class="docs-heading-anchor" href="#Seminar">Seminar</a><a id="Seminar-1"></a><a class="docs-heading-anchor-permalink" href="#Seminar" title="Permalink"></a></h3><ul><li>Presentation about ComplexMixtures.jl and protein-solvent interactions: <a href="https://youtu.be/umSRjsITzyA">https://youtu.be/umSRjsITzyA</a></li></ul><h3 id="Applications"><a class="docs-heading-anchor" href="#Applications">Applications</a><a id="Applications-1"></a><a class="docs-heading-anchor-permalink" href="#Applications" title="Permalink"></a></h3><ul><li><p>A. F. Pereira, V. Piccoli, L. Martínez, <strong>Trifluoroethanol direct interactions with protein backbones destabilize alpha-helices.</strong>  <em>J. Mol. Liq.</em> 365, 120209, 2022. <a href="https://doi.org/10.1016/j.molliq.2022.120209">[Full Text]</a></p></li><li><p>V. Piccoli, L. Martínez, <strong>Ionic liquid solvation of proteins in native and denatured states.</strong>  <em>J. Mol. Liq.</em> 363, 119953, 2022. <a href="http://dx.doi.org/10.1016/j.molliq.2022.119953">[Full Text]</a></p></li><li><p>V. Piccoli, L. Martínez, <strong>Correlated counterion effects in the solvation of proteins by ionic-liquids.</strong> <em>J. Mol. Liq.</em> 320, 114347, 2020. <a href="https://doi.org/10.1016/j.molliq.2020.114347">[Full Text]</a></p></li><li><p>I. P. de Oliveira, L. Martínez, <strong>The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation.</strong> <em>Phys. Chem. Chem. Phys.</em> 22, 354-367, 2020. <a href="https://pubs.rsc.org/en/content/articlelanding/2019/CP/C9CP05196A#!divAbstract">[Full Text]</a></p></li><li><p>I. P. de Oliveira, L. Martínez, <strong>Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea.</strong> <em>Phys. Chem. Chem. Phys.</em> 18, 21797-21808, 2016. <a href="https://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp01789d#!divAbstract">[Full Text]</a></p></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="installation/">Installation »</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 7 August 2023 01:21">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</center><p>In particular, the plot shows that besides being preferentially excluded from the protein surface at high concentrations in the native state, suggesting protein folding stabilization, the interactions with the protein in the denatured states are stronger, leading to denaturation at all concentrations. </p><h2 id="References"><a class="docs-heading-anchor" href="#References">References</a><a id="References-1"></a><a class="docs-heading-anchor-permalink" href="#References" title="Permalink"></a></h2><ul><li><p>L. Martínez, <strong>ComplexMixtures.jl: Investigating the structure of solutions of complex-shaped molecules from a solvent-shell perspective.</strong> <em>J. Mol. Liq.</em> 347, 117945, 2022. <a href="https://doi.org/10.1016/j.molliq.2021.117945">[Full Text]</a></p></li><li><p>L. Martínez, S. Shimizu, <strong>Molecular interpretation of preferential interactions in protein solvation: a solvent-shell perspective by means of minimum-distance distribution functions.</strong> <em>J. Chem. Theor.  Comp.</em> 13, 6358–6372, 2017. <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00599">[Full Text]</a></p></li></ul><h2 id="See-also"><a class="docs-heading-anchor" href="#See-also">See also</a><a id="See-also-1"></a><a class="docs-heading-anchor-permalink" href="#See-also" title="Permalink"></a></h2><h3 id="Seminar"><a class="docs-heading-anchor" href="#Seminar">Seminar</a><a id="Seminar-1"></a><a class="docs-heading-anchor-permalink" href="#Seminar" title="Permalink"></a></h3><ul><li>Presentation about ComplexMixtures.jl and protein-solvent interactions: <a href="https://youtu.be/umSRjsITzyA">https://youtu.be/umSRjsITzyA</a></li></ul><h3 id="Applications"><a class="docs-heading-anchor" href="#Applications">Applications</a><a id="Applications-1"></a><a class="docs-heading-anchor-permalink" href="#Applications" title="Permalink"></a></h3><ul><li><p>A. F. Pereira, V. Piccoli, L. Martínez, <strong>Trifluoroethanol direct interactions with protein backbones destabilize alpha-helices.</strong>  <em>J. Mol. Liq.</em> 365, 120209, 2022. <a href="https://doi.org/10.1016/j.molliq.2022.120209">[Full Text]</a></p></li><li><p>V. Piccoli, L. Martínez, <strong>Ionic liquid solvation of proteins in native and denatured states.</strong>  <em>J. Mol. Liq.</em> 363, 119953, 2022. <a href="http://dx.doi.org/10.1016/j.molliq.2022.119953">[Full Text]</a></p></li><li><p>V. Piccoli, L. Martínez, <strong>Correlated counterion effects in the solvation of proteins by ionic-liquids.</strong> <em>J. Mol. Liq.</em> 320, 114347, 2020. <a href="https://doi.org/10.1016/j.molliq.2020.114347">[Full Text]</a></p></li><li><p>I. P. de Oliveira, L. Martínez, <strong>The shift in urea orientation at protein surfaces at low pH is compatible with a direct mechanism of protein denaturation.</strong> <em>Phys. Chem. Chem. Phys.</em> 22, 354-367, 2020. <a href="https://pubs.rsc.org/en/content/articlelanding/2019/CP/C9CP05196A#!divAbstract">[Full Text]</a></p></li><li><p>I. P. de Oliveira, L. Martínez, <strong>Molecular basis for competitive solvation of the Burkholderia cepacia lipase by sorbitol and urea.</strong> <em>Phys. Chem. Chem. Phys.</em> 18, 21797-21808, 2016. <a href="https://pubs.rsc.org/en/content/articlelanding/2016/cp/c6cp01789d#!divAbstract">[Full Text]</a></p></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="installation/">Installation »</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 7 August 2023 01:29">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/installation/index.html

@@ -9,4 +9,4 @@
 using Plots
 
 # etc ... </code></pre><p>And the script can be run with <code>julia -t auto script.jl</code> (where <code>-t auto</code> allows for multi-threading), or included in julia with <code>julia&gt; include(&quot;./scritp.jl&quot;)</code>, as described in the next section.</p><div class="admonition is-success"><header class="admonition-header">Tip</header><div class="admonition-body"><p>By loading the package with </p><pre><code class="language-julia hljs">using ComplexMixtures</code></pre><p>the most common functions of the package become readily available by their direct name,  for example <code>mddf(...)</code>.</p><p>If you don&#39;t want to bring the functions into the scope of your script, use</p><pre><code class="language-julia hljs">import ComplexMixtures</code></pre><p>Then, the functions of the package are called, for example, using <code>ComplexMixtures.mddf(...)</code>. To avoid having to write <code>ComplexMixtures</code> all the time, define an accronym. For example:</p><pre><code class="language-julia hljs">import ComplexMixtures as CM
-CM.mddf(...)</code></pre></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Introduction</a><a class="docs-footer-nextpage" href="../parallel/">Parallel execution »</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 7 August 2023 01:21">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+CM.mddf(...)</code></pre></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Introduction</a><a class="docs-footer-nextpage" href="../parallel/">Parallel execution »</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 7 August 2023 01:29">Monday 7 August 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>