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Welcome to the Openduck tutorial

Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.

Getting started

Installing openduck

To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).

$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data

Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).

$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.

Contents

This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.

About

No description, website, or topics provided.

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Readme
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
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Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
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Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Welcome to the Openduck tutorial
Openduck is an opensource version of Dynamic Undocking, a particular implementation of steered molecular dynamics (SMD) ment to assess the robustness of protein-ligand complexes through the work needed to bring the main hydrogen bond interaction to the quasi-bound state.
Getting started
Installing openduck
To get started, we will install openduck on an anaconda environment (you can do it in whichever python environment you prefer).
$ git clone git@github.com:CBDD/openduck.git
$ cd openduck
$ conda env create -f environment.yaml
$ conda activate openduck
$ python setup.py install
$ cd ..

Downloading the tutorial data
Once we have openduck up and running, we can start the tutorial by getting the necessary files to run it (including this file).
$ git clone git@github.com:AlvaroSmorras/openduck-tutorial.git
$ cd openduck-tutorial

To run Dynamic Undocking we only need a protein receptor and one or more ligands. In these tutorials, we will use ligands and proteins available in the pdb and configuration files in yaml format.
Contents
This github repo has tutorials for different protocols of openduck, from the default openduck script to using the library to use your own protocols. It is still very work in progress, so any external contributions are welcome.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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