Updates to ACHMC tutorials

docs/build/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-11-12T14:39:50","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-11-12T15:12:50","documenter_version":"1.7.0"}}

docs/build/installation/installation/index.html

@@ -12,4 +12,4 @@
 (virtualenv) $ pip install CTSgetPy
 (virtualenv) $ julia</code></pre><pre><code class="language-julia hljs">julia&gt; using Pkg, PyCall
 julia&gt; ENV[&quot;PYTHON&quot;] = joinpath(ENV[&quot;VIRTUAL_ENV&quot;], &quot;bin&quot;, &quot;python&quot;)
-julia&gt; Pkg.build(&quot;PyCall&quot;)</code></pre><p>Note <code>PyCall.jl</code> will need to be rebuilt whenever you update your Julia version. See <a href="https://github.com/JuliaPy/PyCall.jl">PyCall.jl documentation</a> for more options on setting up Python in Julia.</p><p>See <a href="../python-dependencies/">Exact Python dependencies for RXNMapper</a> for more information.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« MarkovWeightedEFMs.jl</a><a class="docs-footer-nextpage" href="../python-dependencies/">Exact Python dependencies for RXNMapper »</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 1.7.0 on <span class="colophon-date" title="Tuesday 12 November 2024 14:39">Tuesday 12 November 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+julia&gt; Pkg.build(&quot;PyCall&quot;)</code></pre><p>Note <code>PyCall.jl</code> will need to be rebuilt whenever you update your Julia version. See <a href="https://github.com/JuliaPy/PyCall.jl">PyCall.jl documentation</a> for more options on setting up Python in Julia.</p><p>See <a href="../python-dependencies/">Exact Python dependencies for RXNMapper</a> for more information.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« MarkovWeightedEFMs.jl</a><a class="docs-footer-nextpage" href="../python-dependencies/">Exact Python dependencies for RXNMapper »</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 1.7.0 on <span class="colophon-date" title="Tuesday 12 November 2024 15:12">Tuesday 12 November 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

docs/build/installation/python-dependencies/index.html

@@ -74,4 +74,4 @@
 typing_extensions        4.12.2
 tzdata                   2024.1
 urllib3                  2.2.2
-wheel                    0.43.0</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« Getting started</a><a class="docs-footer-nextpage" href="../../tutorials/chmc-standard-metabolic-networks/">CHMC (metabolic networks) »</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 1.7.0 on <span class="colophon-date" title="Tuesday 12 November 2024 14:39">Tuesday 12 November 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+wheel                    0.43.0</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../installation/">« Getting started</a><a class="docs-footer-nextpage" href="../../tutorials/chmc-standard-metabolic-networks/">CHMC (metabolic networks) »</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 1.7.0 on <span class="colophon-date" title="Tuesday 12 November 2024 15:12">Tuesday 12 November 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

docs/build/library/chmc-plots-atomic/index.html

@@ -4,7 +4,7 @@
     fname::String = "";
     view::Bool = false,
     canvas_width::Int64 = 3000,
-    canvas_height::Int64 = 1000</code></pre><p>)</p><p>Plot mapped reaction SMILES string <code>s</code> as an SVG and save to <code>fname</code> if specified.</p><p><code>canvas_width</code> is the width of the SVG.</p><p><code>canvas_height</code> is the height of the SVG.</p><p><code>view = true</code> will plot the SVG assuming a plotting backend is specified. For example, loading the <code>ElectronDisplay</code> package will plot the SVG to an Electron window.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/jchitpin/MarkovWeightedEFMs.jl/blob/e36e0b2350784b4b96a85c6e4f2b8ec0da0351f2/src/chmc-visualization/atomic/atomic.jl#L8-L26">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="MarkovWeightedEFMs.Plots.plot_atomic_chmc" href="#MarkovWeightedEFMs.Plots.plot_atomic_chmc"><code>MarkovWeightedEFMs.Plots.plot_atomic_chmc</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">function plot_atomic_chmc(#
+    canvas_height::Int64 = 1000</code></pre><p>)</p><p>Plot mapped reaction SMILES string <code>s</code> as an SVG and save to <code>fname</code> if specified.</p><p><code>canvas_width</code> is the width of the SVG.</p><p><code>canvas_height</code> is the height of the SVG.</p><p><code>view = true</code> will plot the SVG assuming a plotting backend is specified. For example, loading the <code>ElectronDisplay</code> package will plot the SVG to an Electron window.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/jchitpin/MarkovWeightedEFMs.jl/blob/c39600bf20361836d7a291f4f5e6c4fd972b0abe/src/chmc-visualization/atomic/atomic.jl#L8-L26">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="MarkovWeightedEFMs.Plots.plot_atomic_chmc" href="#MarkovWeightedEFMs.Plots.plot_atomic_chmc"><code>MarkovWeightedEFMs.Plots.plot_atomic_chmc</code></a> — <span class="docstring-category">Function</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">function plot_atomic_chmc(#
     res::CHMCAtomicSummary,
     S::Matrix{Int16},
     mets::Vector{String},
@@ -21,4 +21,4 @@
     } = ((1,0),(0,1)),
     show_all::Bool=false,
     width::Int64=620,
-    height::Int64=310</code></pre><p>)</p><p>Plot atomic cycle-history Markov chain.</p><p><code>S</code> is the m by n stoichiometry matrix.</p><p><code>mets</code> is the vector of metabolite names of length m.</p><p><code>rs</code> is the vector of reaction SMILES strings of length n.</p><p><code>node_label_textsize</code> is the text size of the node labels indexed from <code>T</code>.</p><p><code>edge_label_textsize</code> is the text size of the edge labels taken from <code>T</code>.</p><p><code>arrow_shift</code> is the percentage shift of the arrow head from src to dst.</p><p><code>x_pad</code> is the left/right x coordinate padding of the plotting box.</p><p><code>y_pad</code> is the up/down y coordinate padding of the plotting box.</p><p><code>tfactor</code> scales the distance of the bezier control point relative to the distance of the src and dst nodes.</p><p><code>tangents</code> is the tangent of the src vertex and dst vertex.</p><p><code>show_all=true</code> explicitly plots the upstream transition from all EFMs that pass through the initial state/node <code>I</code>. By default, these arrows stemming from the green nodes are omitted for visual clarity.</p><p><code>width</code> and <code>height</code> specify the plotting window dimensions in pixel units.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/jchitpin/MarkovWeightedEFMs.jl/blob/e36e0b2350784b4b96a85c6e4f2b8ec0da0351f2/src/chmc-visualization/atomic/atomic.jl#L55-L104">source</a></section></article><h2 id="Index"><a class="docs-heading-anchor" href="#Index">Index</a><a id="Index-1"></a><a class="docs-heading-anchor-permalink" href="#Index" title="Permalink"></a></h2><ul></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../chmc-plots-standard/">« Plotting (CHMC)</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 1.7.0 on <span class="colophon-date" title="Tuesday 12 November 2024 14:39">Tuesday 12 November 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    height::Int64=310</code></pre><p>)</p><p>Plot atomic cycle-history Markov chain.</p><p><code>S</code> is the m by n stoichiometry matrix.</p><p><code>mets</code> is the vector of metabolite names of length m.</p><p><code>rs</code> is the vector of reaction SMILES strings of length n.</p><p><code>node_label_textsize</code> is the text size of the node labels indexed from <code>T</code>.</p><p><code>edge_label_textsize</code> is the text size of the edge labels taken from <code>T</code>.</p><p><code>arrow_shift</code> is the percentage shift of the arrow head from src to dst.</p><p><code>x_pad</code> is the left/right x coordinate padding of the plotting box.</p><p><code>y_pad</code> is the up/down y coordinate padding of the plotting box.</p><p><code>tfactor</code> scales the distance of the bezier control point relative to the distance of the src and dst nodes.</p><p><code>tangents</code> is the tangent of the src vertex and dst vertex.</p><p><code>show_all=true</code> explicitly plots the upstream transition from all EFMs that pass through the initial state/node <code>I</code>. By default, these arrows stemming from the green nodes are omitted for visual clarity.</p><p><code>width</code> and <code>height</code> specify the plotting window dimensions in pixel units.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/jchitpin/MarkovWeightedEFMs.jl/blob/c39600bf20361836d7a291f4f5e6c4fd972b0abe/src/chmc-visualization/atomic/atomic.jl#L55-L104">source</a></section></article><h2 id="Index"><a class="docs-heading-anchor" href="#Index">Index</a><a id="Index-1"></a><a class="docs-heading-anchor-permalink" href="#Index" title="Permalink"></a></h2><ul></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../chmc-plots-standard/">« Plotting (CHMC)</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 1.7.0 on <span class="colophon-date" title="Tuesday 12 November 2024 15:12">Tuesday 12 November 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>