Skip to content

Commit

Permalink
docs: render
Browse files Browse the repository at this point in the history
  • Loading branch information
@jmbuhr
jmbuhr committed Oct 25, 2023
1 parent 656ec36 commit 8637990
Show file tree
Hide file tree
Showing 45 changed files with 1,927 additions and 5,345 deletions.
5 changes: 0 additions & 5 deletions _reference/utils.qmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -86,11 +86,6 @@ Returns dissociation energy E_dissoc for a set of two atomnames.

Returns the path to the gromacs installation

This does not check if the installation is valid.
It just returns the path to the gromacs data directory.
If `gmx` is not executable it still returns the default
gromacs data directory in `/usr/share/gromacs`.

### get_shell_stdout { #kimmdy.utils.get_shell_stdout }

`utils.get_shell_stdout(s)`
Expand Down
180 changes: 41 additions & 139 deletions docs/_reference/analysis.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.176">
<meta name="generator" content="quarto-1.3.450">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -50,11 +50,6 @@
"panel-placement": "end",
"type": "overlay",
"limit": 20,
"keyboard-shortcut": [
"f",
"/",
"s"
],
"language": {
"search-no-results-text": "No results",
"search-matching-documents-text": "matching documents",
Expand All @@ -78,7 +73,7 @@
<header id="quarto-header" class="headroom fixed-top">
<nav class="navbar navbar-expand-lg navbar-dark ">
<div class="navbar-container container-fluid">
<div class="navbar-brand-container mx-auto">
<div class="navbar-brand-container">
<a class="navbar-brand" href="../index.html">
<span class="navbar-title">KIMMDY</span>
</a>
Expand All @@ -102,18 +97,17 @@
<span class="menu-text">Reference</span></a>
</li>
</ul>
</div> <!-- /navcollapse -->
<div class="quarto-navbar-tools tools-wide">
<div class="quarto-navbar-tools ms-auto tools-wide">
<div class="dropdown">
<a href="" title="" id="quarto-navigation-tool-dropdown-0" class="quarto-navigation-tool dropdown-toggle px-1" data-bs-toggle="dropdown" aria-expanded="false" aria-label=""><i class="bi bi-github"></i></a>
<ul class="dropdown-menu dropdown-menu-end" aria-labelledby="quarto-navigation-tool-dropdown-0">
<li>
<a class="dropdown-item quarto-navbar-tools-item" href="https://github.com/hits-mbm-dev/kimmdy">
<a class="dropdown-item quarto-navbar-tools ms-auto-item" href="https://github.com/hits-mbm-dev/kimmdy">
Source Code
</a>
</li>
<li>
<a class="dropdown-item quarto-navbar-tools-item" href="https://github.com/hits-mbm-dev/kimmdy/issues/new">
<a class="dropdown-item quarto-navbar-tools ms-auto-item" href="https://github.com/hits-mbm-dev/kimmdy/issues/new">
Report a Bug
</a>
</li>
Expand All @@ -126,16 +120,17 @@
</div>
</a>
</div>
</div> <!-- /navcollapse -->
</div> <!-- /container-fluid -->
</nav>
<nav class="quarto-secondary-nav">
<div class="container-fluid d-flex">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Modules</a></li><li class="breadcrumb-item"><a href="../_reference/analysis.html">analysis</a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="../_reference/index.html">Reference</a></li><li class="breadcrumb-item"><a href="../_reference/constants.html">Modules</a></li><li class="breadcrumb-item"><a href="../_reference/analysis.html">analysis</a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
</div>
</nav>
</header>
Expand All @@ -162,70 +157,70 @@
</li>
<li class="sidebar-item sidebar-item-section">
<div class="sidebar-item-container">
<a href="../guide/tutorials/index.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Tutorials</span></a>
<a href="../guide/how_to/index.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">How-To</span></a>
<a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="false" aria-label="Toggle section">
<i class="bi bi-chevron-right ms-2"></i>
</a>
</div>
<ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth2 ">
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/tutorials/colbuilder.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">1. Run KIMMDY from Colbuilder fibril</span></a>
<a href="../guide/how_to/contribute.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Contribute</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/tutorials/getting-started.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">0. Getting Started</span></a>
<a href="../guide/how_to/hcp.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">High Performance Computing</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/tutorials/write-plugin.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">2. Writing a Reaction Plugin</span></a>
<a href="../guide/how_to/options.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">KIMMDY Options</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/plugins.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Write Reaction Plugins</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/topology.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Visualize Topologies</span></a>
</div>
</li>
</ul>
</li>
<li class="sidebar-item sidebar-item-section">
<div class="sidebar-item-container">
<a href="../guide/how_to/index.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">How-To</span></a>
<a href="../guide/tutorials/index.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Tutorials</span></a>
<a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="false" aria-label="Toggle section">
<i class="bi bi-chevron-right ms-2"></i>
</a>
</div>
<ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth2 ">
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/contribute.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Contribute</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/hcp.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">High Performance Computing</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/options.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">KIMMDY Options</span></a>
<a href="../guide/tutorials/colbuilder.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">1. Run KIMMDY from Colbuilder fibril</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/plugins.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Write Reaction Plugins</span></a>
<a href="../guide/tutorials/getting-started.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">0. Getting Started</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../guide/how_to/topology.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">Visualize Topologies</span></a>
<a href="../guide/tutorials/write-plugin.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">2. Writing a Reaction Plugin</span></a>
</div>
</li>
</ul>
Expand Down Expand Up @@ -883,33 +878,6 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
}
}
}
const toggleGiscusIfUsed = (isAlternate, darkModeDefault) => {
const baseTheme = document.querySelector('#giscus-base-theme')?.value ?? 'light';
const alternateTheme = document.querySelector('#giscus-alt-theme')?.value ?? 'dark';
let newTheme = '';
if(darkModeDefault) {
newTheme = isAlternate ? baseTheme : alternateTheme;
} else {
newTheme = isAlternate ? alternateTheme : baseTheme;
}
const changeGiscusTheme = () => {
// From: https://github.com/giscus/giscus/issues/336
const sendMessage = (message) => {
const iframe = document.querySelector('iframe.giscus-frame');
if (!iframe) return;
iframe.contentWindow.postMessage({ giscus: message }, 'https://giscus.app');
}
sendMessage({
setConfig: {
theme: newTheme
}
});
}
const isGiscussLoaded = window.document.querySelector('iframe.giscus-frame') !== null;
if (isGiscussLoaded) {
changeGiscusTheme();
}
}
const toggleColorMode = (alternate) => {
// Switch the stylesheets
const alternateStylesheets = window.document.querySelectorAll('link.quarto-color-scheme.quarto-color-alternate');
Expand Down Expand Up @@ -976,15 +944,13 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
return localAlternateSentinel;
}
}
const darkModeDefault = false;
let localAlternateSentinel = darkModeDefault ? 'alternate' : 'default';
let localAlternateSentinel = 'default';
// Dark / light mode switch
window.quartoToggleColorScheme = () => {
// Read the current dark / light value
let toAlternate = !hasAlternateSentinel();
toggleColorMode(toAlternate);
setStyleSentinel(toAlternate);
toggleGiscusIfUsed(toAlternate, darkModeDefault);
};
// Ensure there is a toggle, if there isn't float one in the top right
if (window.document.querySelector('.quarto-color-scheme-toggle') === null) {
Expand Down Expand Up @@ -1063,9 +1029,10 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
Expand All @@ -1075,17 +1042,8 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start',
placement: 'bottom-start'
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
Expand All @@ -1099,60 +1057,6 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
const processXRef = (id, note) => {
if (id.startsWith('sec-')) {
// Special case sections, only their first couple elements
const container = document.createElement("div");
if (note.children && note.children.length > 2) {
for (let i = 0; i < 2; i++) {
container.appendChild(note.children[i].cloneNode(true));
}
return container.innerHTML
} else {
return note.innerHTML;
}
} else {
return note.innerHTML;
}
}
for (var i=0; i<xrefs.length; i++) {
const xref = xrefs[i];
tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
try { hash = new URL(url).hash; } catch {}
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note);
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
Expand Down Expand Up @@ -1195,7 +1099,6 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
Expand Down Expand Up @@ -1296,5 +1199,4 @@ <h4 class="anchored" data-anchor-id="parameters-6">Parameters</h4>




</body></html>
Loading

0 comments on commit 8637990

Please sign in to comment.