build based on 958ac6f

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.1","generation_timestamp":"2024-02-15T12:23:45","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.10.1","generation_timestamp":"2024-02-20T19:30:13","documenter_version":"1.2.1"}}

dev/assets/scripts/example2/script3.jl

@@ -10,12 +10,12 @@ using PDBTools
 # contributions of each mer of the polymer into its chemical groups
 
 # Chemical groups of the polymer monomers, defined by the atom types:
-groups = Dict(
-    L"\textrm{CH_3}" => ["CF","HF1","HF2","HF3"], # methyles
+groups = (
+    "CH_3" => ["CF","HF1","HF2","HF3"], # methyles
     "CO" => ["OE1","CD"], # carbonyl
-    L"\textrm{NH_2}" => ["NE2","HE22","HE21"], # amine 
-    L"\textrm{CHCH_2}" => ["C","H2","H1","CA","HA"], # backbone
-    L"\textrm{CH_3}" => ["CL","HL1","HL2","HL3"], # terminal methyles
+    "NH_2" => ["NE2","HE22","HE21"], # amine 
+    "CHCH_2" => ["C","H2","H1","CA","HA"], # backbone
+    "CH_3" => ["CL","HL1","HL2","HL3"], # terminal methyles
 )
 
 system = readPDB("./equilibrated.pdb")
@@ -25,15 +25,15 @@ results = load("./mddf.json")
 # Here we split the polymer in residues, to extract the contribution of 
 # each chemical group of each polymer mer independently
 group_contribs = Vector{Float64}[]
-labels = String[]
+labels = LaTeXString[]
 for (imer, mer) in enumerate(eachresidue(acr))
     for (group_label, group_atoms) in pairs(groups)
         # only first residue has a terminal CH3
-        if imer != 1 && group_label == L"\textrm{CH_3}" 
+        if imer != 1 && group_label == "CH_3" 
             continue
         end
         # only last residue has a terminal CH3
-        if imer != 5 && group_label == L"\textrm{CH_3}" 
+        if imer != 5 && group_label == "CH_3" 
             continue
         end
         # Filter the atoms of this mer that belong to the group
@@ -44,8 +44,8 @@ for (imer, mer) in enumerate(eachresidue(acr))
         atoms_contrib = movavg(atoms_contrib; n = 10).x
         # Add contributions to the group contributions list
         push!(group_contribs, atoms_contrib)
-        # Push label to label list
-        push!(labels,group_label)
+        # Push label to label list, using LaTeX formatting
+        push!(labels,latexstring("\\textrm{$group_label}"))
     end
 end
 

dev/contrib/index.html

@@ -43,4 +43,4 @@
 julia> results = load(dir*"/protein_EMI.json"); # load pre-calculated results
 
 julia> contributions(results, SoluteGroup(["CA", "CB"])) # contribution of CA and CB atoms to the MDDF
-</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/ComplexMixtures.jl/blob/104aeb7be6942de258f9174aeb1ae1922ff32e29/src/tools/contributions.jl#L1-L43">source</a></section></article></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><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 1.2.1 on <span class="colophon-date" title="Thursday 15 February 2024 12:23">Thursday 15 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/m3g/ComplexMixtures.jl/blob/958ac6fd4ffb03081b01861a2342b384cddf92b7/src/tools/contributions.jl#L1-L43">source</a></section></article></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><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 1.2.1 on <span class="colophon-date" title="Tuesday 20 February 2024 19:30">Tuesday 20 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/example1/index.html

@@ -181,4 +181,4 @@
 <img width=100% src="https://github.com/m3g/ComplexMixturesExamples/raw/main/Protein_in_Glycerol/Density3D/density3D_final.png">
 </center><p>In the figure on the left, the points in space around the protein are selected with the following properties: distance from the protein smaller than 2.0Å and relative contribution to the MDDF at the corresponding distance of at least 10% of the maximum contribution. Thus, we are selecting the regions of the protein corresponding to the most stable hydrogen-bonding interactions. The color of the points is the contribution to the MDDF, from blue to red. Thus, the most reddish-points corresponds to the regions where the most stable hydrogen bonds were formed. We have marked two regions here, on opposite sides of the protein, with arrows.</p><p>Clicking on those points we obtain which are the atoms of the protein contributing to the MDDF at that region. In particular, the arrow on the right points to the strongest red region, which corresponds to an Aspartic acid. These residues are shown explicitly under the density (represented as a transparent surface) on the figure in the center.</p><p>The figure on the right displays, overlapped with the hydrogen-bonding residues, the most important contributions to the second peak of the distribution, corresponding to distances from the protein between 2.0 and 3.5Å. Notably, the regions involved are different from the ones forming hydrogen bonds, indicating that non-specific interactions with the protein (and not a second solvation shell) are responsible for the second peak. </p><h3 id="How-to-run-this-example:"><a class="docs-heading-anchor" href="#How-to-run-this-example:">How to run this example:</a><a id="How-to-run-this-example:-1"></a><a class="docs-heading-anchor-permalink" href="#How-to-run-this-example:" title="Permalink"></a></h3><p>Assuming that the input files are available in the script directory, just run the script with:</p><pre><code class="language-bash hljs">julia density3D.jl</code></pre><p>Alternatively, open Julia and copy/paste or the commands in <code>density3D.jl</code> or use <code>include(&quot;./density3D.jl&quot;)</code>. These options will allow you to remain on the Julia section with access to the <code>grid</code> data structure that was generated and corresponds to the output <code>grid.pdb</code> file. </p><p>This will create the <code>grid.pdb</code> file. <a href="https://raw.githubusercontent.com/m3g/ComplexMixturesExamples/main/Protein_in_Glycerol/Density3D/grid.vmd">Here</a> we provide a previously setup VMD session that contains the data with the visualization choices used to generate the figure above. Load it with:</p><pre><code class="language-bash hljs">vmd -e grid.vmd</code></pre><p>A short tutorial video showing how to open the input and output PDB files in VMD and produce images of the density is available here: </p><center>
 <iframe width="560" style="height:315px" src="https://www.youtube.com/embed/V4Py44IKDh8" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
-</center></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../examples/">« Examples:</a><a class="docs-footer-nextpage" href="../example2/">◦ Polyacrylamide in DMF »</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 1.2.1 on <span class="colophon-date" title="Thursday 15 February 2024 12:23">Thursday 15 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</center></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../examples/">« Examples:</a><a class="docs-footer-nextpage" href="../example2/">◦ Polyacrylamide in DMF »</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 1.2.1 on <span class="colophon-date" title="Tuesday 20 February 2024 19:30">Tuesday 20 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/example2/index.html

@@ -184,12 +184,12 @@
 # contributions of each mer of the polymer into its chemical groups
 
 # Chemical groups of the polymer monomers, defined by the atom types:
-groups = Dict(
-    L"\textrm{CH_3}" => ["CF","HF1","HF2","HF3"], # methyles
+groups = (
+    "CH_3" => ["CF","HF1","HF2","HF3"], # methyles
     "CO" => ["OE1","CD"], # carbonyl
-    L"\textrm{NH_2}" => ["NE2","HE22","HE21"], # amine 
-    L"\textrm{CHCH_2}" => ["C","H2","H1","CA","HA"], # backbone
-    L"\textrm{CH_3}" => ["CL","HL1","HL2","HL3"], # terminal methyles
+    "NH_2" => ["NE2","HE22","HE21"], # amine 
+    "CHCH_2" => ["C","H2","H1","CA","HA"], # backbone
+    "CH_3" => ["CL","HL1","HL2","HL3"], # terminal methyles
 )
 
 system = readPDB("./equilibrated.pdb")
@@ -199,15 +199,15 @@
 # Here we split the polymer in residues, to extract the contribution of 
 # each chemical group of each polymer mer independently
 group_contribs = Vector{Float64}[]
-labels = String[]
+labels = LaTeXString[]
 for (imer, mer) in enumerate(eachresidue(acr))
     for (group_label, group_atoms) in pairs(groups)
         # only first residue has a terminal CH3
-        if imer != 1 && group_label == L"\textrm{CH_3}" 
+        if imer != 1 && group_label == "CH_3" 
             continue
         end
         # only last residue has a terminal CH3
-        if imer != 5 && group_label == L"\textrm{CH_3}" 
+        if imer != 5 && group_label == "CH_3" 
             continue
         end
         # Filter the atoms of this mer that belong to the group
@@ -218,8 +218,8 @@
         atoms_contrib = movavg(atoms_contrib; n = 10).x
         # Add contributions to the group contributions list
         push!(group_contribs, atoms_contrib)
-        # Push label to label list
-        push!(labels,group_label)
+        # Push label to label list, using LaTeX formatting
+        push!(labels,latexstring("\\textrm{$group_label}"))
     end
 end
 
@@ -245,4 +245,4 @@
 savefig("./map2D_acr.png")
 println(&quot;Plot saved to map2D_acr.png&quot;)</code></pre></details><br><h4 id="Output-3"><a class="docs-heading-anchor" href="#Output-3">Output</a><a class="docs-heading-anchor-permalink" href="#Output-3" title="Permalink"></a></h4><p>The terminal methyl groups interact strongly with DMF, and strong local density augmentations are visible in particular on the amine groups. These occur at less than 2.0Angs and are characteristic of hydrogen-bond interactions. Interestingly, the DMF molecules are excluded from the aliphatic and carbonyl groups of the polymer, relative to the other groups.</p><p>Finally, it is noticeable that the central mer is more weakly solvated by DMF than the mers approaching the extremes of the polymer chain. This is likely a result of the partial folding of the polymer, that protects that central mers from the solvent in a fraction of the polymer configurations.</p><center>
 <img width=70% src="https://github.com/m3g/ComplexMixturesExamples/raw/main/Protein_in_Glycerol/Density2D/density2D.png">
-</center><h3 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></h3><p>Molecules built with JSME: B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) <a href="http://biomodel.uah.es/en/DIY/JSME/draw.en.htm">http://biomodel.uah.es/en/DIY/JSME/draw.en.htm</a></p><p>The system was built with <a href="http://m3g.iqm.unicamp.br/packmol">Packmol</a>.</p><p>The simulations were perfomed with <a href="https://www.ks.uiuc.edu/Research/namd/">NAMD</a>, with <a href="https://www.charmm.org">CHARMM36</a> parameters. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../example1/">« ◦ Protein in water/glycerol</a><a class="docs-footer-nextpage" href="../example3/">◦ POPC membrane in water/ethanol »</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 1.2.1 on <span class="colophon-date" title="Thursday 15 February 2024 12:23">Thursday 15 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</center><h3 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></h3><p>Molecules built with JSME: B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) <a href="http://biomodel.uah.es/en/DIY/JSME/draw.en.htm">http://biomodel.uah.es/en/DIY/JSME/draw.en.htm</a></p><p>The system was built with <a href="http://m3g.iqm.unicamp.br/packmol">Packmol</a>.</p><p>The simulations were perfomed with <a href="https://www.ks.uiuc.edu/Research/namd/">NAMD</a>, with <a href="https://www.charmm.org">CHARMM36</a> parameters. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../example1/">« ◦ Protein in water/glycerol</a><a class="docs-footer-nextpage" href="../example3/">◦ POPC membrane in water/ethanol »</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 1.2.1 on <span class="colophon-date" title="Tuesday 20 February 2024 19:30">Tuesday 20 February 2024</span>. Using Julia version 1.10.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>