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kh01734 committed Nov 7, 2024
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49 changes: 14 additions & 35 deletions 404.html
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<!DOCTYPE HTML>
<html lang="en" class="light" dir="ltr">
<html lang="en" class="light sidebar-visible" dir="ltr">
<head>
<!-- Book generated using mdBook -->
<meta charset="UTF-8">
Expand All @@ -8,7 +8,7 @@


<!-- Custom HTML head -->

<meta name="description" content="">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#ffffff">
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<!-- Custom theme stylesheets -->

</head>
<body class="sidebar-visible no-js">
<body>
<div id="body-container">
<!-- Provide site root to javascript -->
<script>
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var theme;
try { theme = localStorage.getItem('mdbook-theme'); } catch(e) { }
if (theme === null || theme === undefined) { theme = default_theme; }
var html = document.querySelector('html');
const html = document.documentElement;
html.classList.remove('light')
html.classList.add(theme);
var body = document.querySelector('body');
body.classList.remove('no-js')
body.classList.add('js');
html.classList.add("js");
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<input type="checkbox" id="sidebar-toggle-anchor" class="hidden">

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<script>
var body = document.querySelector('body');
var sidebar = null;
var sidebar_toggle = document.getElementById("sidebar-toggle-anchor");
if (document.body.clientWidth >= 1080) {
Expand All @@ -83,45 +80,27 @@
sidebar = 'hidden';
}
sidebar_toggle.checked = sidebar === 'visible';
body.classList.remove('sidebar-visible');
body.classList.add("sidebar-" + sidebar);
html.classList.remove('sidebar-visible');
html.classList.add("sidebar-" + sidebar);
</script>

<nav id="sidebar" class="sidebar" aria-label="Table of contents">
<div class="sidebar-scrollbox">
<ol class="chapter"><li class="chapter-item expanded affix "><a href="index.html">PaCS-Toolkit User Guide</a></li><li class="chapter-item expanded "><a href="quickstart.html"><strong aria-hidden="true">1.</strong> Quick Start</a></li><li class="chapter-item expanded "><a href="install.html"><strong aria-hidden="true">2.</strong> Install</a></li><li class="chapter-item expanded "><a href="mdrun.html"><strong aria-hidden="true">3.</strong> mdrun</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/overview.html"><strong aria-hidden="true">3.1.</strong> Overview</a></li><li class="chapter-item expanded "><a href="mdrun/basic.html"><strong aria-hidden="true">3.2.</strong> Basic</a></li><li class="chapter-item expanded "><a href="mdrun/simulator.html"><strong aria-hidden="true">3.3.</strong> Simulator</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer.html"><strong aria-hidden="true">3.4.</strong> Analyzer</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/analyzer/rmsd.html"><strong aria-hidden="true">3.4.1.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/target.html"><strong aria-hidden="true">3.4.2.</strong> target</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/dissociation.html"><strong aria-hidden="true">3.4.3.</strong> dissociation</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/association.html"><strong aria-hidden="true">3.4.4.</strong> association</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/a_d.html"><strong aria-hidden="true">3.4.5.</strong> a_d</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/ee.html"><strong aria-hidden="true">3.4.6.</strong> ee</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/template.html"><strong aria-hidden="true">3.4.7.</strong> template</a></li></ol></li><li class="chapter-item expanded "><a href="mdrun/inputfile.html"><strong aria-hidden="true">3.5.</strong> Input file</a></li><li class="chapter-item expanded "><a href="mdrun/reference.html"><strong aria-hidden="true">3.6.</strong> Reference</a></li></ol></li><li class="chapter-item expanded "><a href="rmmol.html"><strong aria-hidden="true">4.</strong> rmmol</a></li><li class="chapter-item expanded "><a href="rmfile.html"><strong aria-hidden="true">5.</strong> rmfile</a></li><li class="chapter-item expanded "><a href="fit.html"><strong aria-hidden="true">6.</strong> fit</a></li><li class="chapter-item expanded "><a href="genrepresent.html"><strong aria-hidden="true">7.</strong> genrepresent</a></li><li class="chapter-item expanded "><a href="gencom.html"><strong aria-hidden="true">8.</strong> gencom</a></li><li class="chapter-item expanded "><a href="genfeature.html"><strong aria-hidden="true">9.</strong> genfeature</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="genfeature/comdist.html"><strong aria-hidden="true">9.1.</strong> comdist</a></li><li class="chapter-item expanded "><a href="genfeature/comvec.html"><strong aria-hidden="true">9.2.</strong> comvec</a></li><li class="chapter-item expanded "><a href="genfeature/rmsd.html"><strong aria-hidden="true">9.3.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="genfeature/xyz.html"><strong aria-hidden="true">9.4.</strong> xyz</a></li></ol></li><li class="chapter-item expanded "><a href="FAQ.html"><strong aria-hidden="true">10.</strong> FAQ</a></li></ol>
</div>
<!-- populated by js -->
<div class="sidebar-scrollbox"></div>
<noscript>
<iframe class="sidebar-iframe-outer" src="toc.html"></iframe>
</noscript>
<div id="sidebar-resize-handle" class="sidebar-resize-handle">
<div class="sidebar-resize-indicator"></div>
</div>
</nav>

<!-- Track and set sidebar scroll position -->
<script>
var sidebarScrollbox = document.querySelector('#sidebar .sidebar-scrollbox');
sidebarScrollbox.addEventListener('click', function(e) {
if (e.target.tagName === 'A') {
sessionStorage.setItem('sidebar-scroll', sidebarScrollbox.scrollTop);
}
}, { passive: true });
var sidebarScrollTop = sessionStorage.getItem('sidebar-scroll');
sessionStorage.removeItem('sidebar-scroll');
if (sidebarScrollTop) {
// preserve sidebar scroll position when navigating via links within sidebar
sidebarScrollbox.scrollTop = sidebarScrollTop;
} else {
// scroll sidebar to current active section when navigating via "next/previous chapter" buttons
var activeSection = document.querySelector('#sidebar .active');
if (activeSection) {
activeSection.scrollIntoView({ block: 'center' });
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}
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<script async src="toc.js"></script>

<div id="page-wrapper" class="page-wrapper">

<div class="page">
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49 changes: 14 additions & 35 deletions FAQ.html
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@@ -1,13 +1,13 @@
<!DOCTYPE HTML>
<html lang="en" class="light" dir="ltr">
<html lang="en" class="light sidebar-visible" dir="ltr">
<head>
<!-- Book generated using mdBook -->
<meta charset="UTF-8">
<title>FAQ - PaCS-Toolkit User Guide</title>


<!-- Custom HTML head -->

<meta name="description" content="">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="theme-color" content="#ffffff">
Expand All @@ -31,7 +31,7 @@
<!-- Custom theme stylesheets -->

</head>
<body class="sidebar-visible no-js">
<body>
<div id="body-container">
<!-- Provide site root to javascript -->
<script>
Expand Down Expand Up @@ -60,19 +60,16 @@
var theme;
try { theme = localStorage.getItem('mdbook-theme'); } catch(e) { }
if (theme === null || theme === undefined) { theme = default_theme; }
var html = document.querySelector('html');
const html = document.documentElement;
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html.classList.add(theme);
var body = document.querySelector('body');
body.classList.remove('no-js')
body.classList.add('js');
html.classList.add("js");
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<input type="checkbox" id="sidebar-toggle-anchor" class="hidden">

<!-- Hide / unhide sidebar before it is displayed -->
<script>
var body = document.querySelector('body');
var sidebar = null;
var sidebar_toggle = document.getElementById("sidebar-toggle-anchor");
if (document.body.clientWidth >= 1080) {
Expand All @@ -82,45 +79,27 @@
sidebar = 'hidden';
}
sidebar_toggle.checked = sidebar === 'visible';
body.classList.remove('sidebar-visible');
body.classList.add("sidebar-" + sidebar);
html.classList.remove('sidebar-visible');
html.classList.add("sidebar-" + sidebar);
</script>

<nav id="sidebar" class="sidebar" aria-label="Table of contents">
<div class="sidebar-scrollbox">
<ol class="chapter"><li class="chapter-item expanded affix "><a href="index.html">PaCS-Toolkit User Guide</a></li><li class="chapter-item expanded "><a href="quickstart.html"><strong aria-hidden="true">1.</strong> Quick Start</a></li><li class="chapter-item expanded "><a href="install.html"><strong aria-hidden="true">2.</strong> Install</a></li><li class="chapter-item expanded "><a href="mdrun.html"><strong aria-hidden="true">3.</strong> mdrun</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/overview.html"><strong aria-hidden="true">3.1.</strong> Overview</a></li><li class="chapter-item expanded "><a href="mdrun/basic.html"><strong aria-hidden="true">3.2.</strong> Basic</a></li><li class="chapter-item expanded "><a href="mdrun/simulator.html"><strong aria-hidden="true">3.3.</strong> Simulator</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer.html"><strong aria-hidden="true">3.4.</strong> Analyzer</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="mdrun/analyzer/rmsd.html"><strong aria-hidden="true">3.4.1.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/target.html"><strong aria-hidden="true">3.4.2.</strong> target</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/dissociation.html"><strong aria-hidden="true">3.4.3.</strong> dissociation</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/association.html"><strong aria-hidden="true">3.4.4.</strong> association</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/a_d.html"><strong aria-hidden="true">3.4.5.</strong> a_d</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/ee.html"><strong aria-hidden="true">3.4.6.</strong> ee</a></li><li class="chapter-item expanded "><a href="mdrun/analyzer/template.html"><strong aria-hidden="true">3.4.7.</strong> template</a></li></ol></li><li class="chapter-item expanded "><a href="mdrun/inputfile.html"><strong aria-hidden="true">3.5.</strong> Input file</a></li><li class="chapter-item expanded "><a href="mdrun/reference.html"><strong aria-hidden="true">3.6.</strong> Reference</a></li></ol></li><li class="chapter-item expanded "><a href="rmmol.html"><strong aria-hidden="true">4.</strong> rmmol</a></li><li class="chapter-item expanded "><a href="rmfile.html"><strong aria-hidden="true">5.</strong> rmfile</a></li><li class="chapter-item expanded "><a href="fit.html"><strong aria-hidden="true">6.</strong> fit</a></li><li class="chapter-item expanded "><a href="genrepresent.html"><strong aria-hidden="true">7.</strong> genrepresent</a></li><li class="chapter-item expanded "><a href="gencom.html"><strong aria-hidden="true">8.</strong> gencom</a></li><li class="chapter-item expanded "><a href="genfeature.html"><strong aria-hidden="true">9.</strong> genfeature</a></li><li><ol class="section"><li class="chapter-item expanded "><a href="genfeature/comdist.html"><strong aria-hidden="true">9.1.</strong> comdist</a></li><li class="chapter-item expanded "><a href="genfeature/comvec.html"><strong aria-hidden="true">9.2.</strong> comvec</a></li><li class="chapter-item expanded "><a href="genfeature/rmsd.html"><strong aria-hidden="true">9.3.</strong> rmsd</a></li><li class="chapter-item expanded "><a href="genfeature/xyz.html"><strong aria-hidden="true">9.4.</strong> xyz</a></li></ol></li><li class="chapter-item expanded "><a href="FAQ.html" class="active"><strong aria-hidden="true">10.</strong> FAQ</a></li></ol>
</div>
<!-- populated by js -->
<div class="sidebar-scrollbox"></div>
<noscript>
<iframe class="sidebar-iframe-outer" src="toc.html"></iframe>
</noscript>
<div id="sidebar-resize-handle" class="sidebar-resize-handle">
<div class="sidebar-resize-indicator"></div>
</div>
</nav>

<!-- Track and set sidebar scroll position -->
<script>
var sidebarScrollbox = document.querySelector('#sidebar .sidebar-scrollbox');
sidebarScrollbox.addEventListener('click', function(e) {
if (e.target.tagName === 'A') {
sessionStorage.setItem('sidebar-scroll', sidebarScrollbox.scrollTop);
}
}, { passive: true });
var sidebarScrollTop = sessionStorage.getItem('sidebar-scroll');
sessionStorage.removeItem('sidebar-scroll');
if (sidebarScrollTop) {
// preserve sidebar scroll position when navigating via links within sidebar
sidebarScrollbox.scrollTop = sidebarScrollTop;
} else {
// scroll sidebar to current active section when navigating via "next/previous chapter" buttons
var activeSection = document.querySelector('#sidebar .active');
if (activeSection) {
activeSection.scrollIntoView({ block: 'center' });
}
}
</script>
<script async src="toc.js"></script>

<div id="page-wrapper" class="page-wrapper">

<div class="page">
<div id="menu-bar-hover-placeholder"></div>
<div id="menu-bar-hover-placeholder"></div>
<div id="menu-bar" class="menu-bar sticky">
<div class="left-buttons">
<label id="sidebar-toggle" class="icon-button" for="sidebar-toggle-anchor" title="Toggle Table of Contents" aria-label="Toggle Table of Contents" aria-controls="sidebar">
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14 changes: 9 additions & 5 deletions book.js
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,7 @@ function playground_text(playground, hidden = true) {
}

var clipButton = document.createElement('button');
clipButton.className = 'fa fa-copy clip-button';
clipButton.className = 'clip-button';
clipButton.title = 'Copy to clipboard';
clipButton.setAttribute('aria-label', clipButton.title);
clipButton.innerHTML = '<i class=\"tooltiptext\"></i>';
Expand Down Expand Up @@ -258,7 +258,7 @@ function playground_text(playground, hidden = true) {

if (window.playground_copyable) {
var copyCodeClipboardButton = document.createElement('button');
copyCodeClipboardButton.className = 'fa fa-copy clip-button';
copyCodeClipboardButton.className = 'clip-button';
copyCodeClipboardButton.innerHTML = '<i class="tooltiptext"></i>';
copyCodeClipboardButton.title = 'Copy to clipboard';
copyCodeClipboardButton.setAttribute('aria-label', copyCodeClipboardButton.title);
Expand Down Expand Up @@ -289,6 +289,10 @@ function playground_text(playground, hidden = true) {
var themeToggleButton = document.getElementById('theme-toggle');
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var themeColorMetaTag = document.querySelector('meta[name="theme-color"]');
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var stylesheets = {
ayuHighlight: document.querySelector("[href$='ayu-highlight.css']"),
tomorrowNight: document.querySelector("[href$='tomorrow-night.css']"),
Expand Down Expand Up @@ -317,7 +321,7 @@ function playground_text(playground, hidden = true) {
function get_theme() {
var theme;
try { theme = localStorage.getItem('mdbook-theme'); } catch (e) { }
if (theme === null || theme === undefined) {
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return default_theme;
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Expand Down Expand Up @@ -597,12 +601,12 @@ function playground_text(playground, hidden = true) {

function hideTooltip(elem) {
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function showTooltip(elem, msg) {
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elem.className = 'fa fa-copy tooltipped';
elem.className = 'clip-button tooltipped';
}

var clipboardSnippets = new ClipboardJS('.clip-button', {
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