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<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>MD Simulation Pipeline</title>
<link rel="stylesheet" href="../css/styles.css">
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<body>
<div class="container">
<!-- Header -->
<header class="header">
<div class="header-content">
<h1><i class="fas fa-atom"></i> MD Simulation Pipeline</h1>
<p>Molecular Dynamics Simulation Setup and File Generation</p>
</div>
</header>
<!-- Navigation Tabs -->
<nav class="tab-navigation">
<button class="tab-button active" data-tab="protein-loading">
<i class="fas fa-upload"></i> Protein Loading
</button>
<button class="tab-button" data-tab="fill-missing">
<i class="fas fa-puzzle-piece"></i> Fill Missing Residues
</button>
<button class="tab-button" data-tab="structure-prep">
<i class="fas fa-tools"></i> Structure Preparation
</button>
<button class="tab-button" data-tab="simulation-params">
<i class="fas fa-cogs"></i> Simulation Parameters
</button>
<button class="tab-button" data-tab="simulation-steps">
<i class="fas fa-list-ol"></i> Simulation Steps
</button>
<button class="tab-button" data-tab="file-generation">
<i class="fas fa-file-download"></i> Generate Files
</button>
<button class="tab-button" data-tab="plumed">
<i class="fas fa-chart-line"></i> PLUMED
</button>
</nav>
<!-- Main Content -->
<main class="main-content">
<!-- Protein Loading Tab -->
<div id="protein-loading" class="tab-content active">
<div class="card">
<h2><i class="fas fa-dna"></i> Protein Structure Input</h2>
<div class="input-methods">
<div class="method-option">
<h3><i class="fas fa-file-upload"></i> Upload PDB File</h3>
<div class="file-upload-area" id="file-upload-area">
<i class="fas fa-cloud-upload-alt"></i>
<p>Drag and drop your PDB file here or click to browse</p>
<input type="file" id="pdb-file" accept=".pdb,.ent" style="display: none;">
<button type="button" class="btn btn-secondary" id="choose-file-btn">
Choose File
</button>
</div>
<div id="file-info" class="file-info" style="display: none;">
<p><strong>Selected file:</strong> <span id="file-name"></span></p>
<p><strong>Size:</strong> <span id="file-size"></span></p>
</div>
</div>
<div class="divider">
<span>OR</span>
</div>
<div class="method-option">
<h3><i class="fas fa-database"></i> Fetch from PDB</h3>
<div class="pdb-fetch">
<div class="input-group">
<label for="pdb-id">PDB ID:</label>
<input type="text" id="pdb-id" placeholder="e.g., 1CRN, 1HTM" maxlength="4">
<button type="button" class="btn btn-primary" id="fetch-pdb">
<i class="fas fa-download"></i> Fetch
</button>
</div>
<div id="pdb-status" class="status-message"></div>
</div>
</div>
</div>
<div class="protein-preview" id="protein-preview" style="display: none;">
<h3><i class="fas fa-eye"></i> Protein Preview</h3>
<div class="preview-content">
<div class="protein-info">
<p><strong>Structure ID:</strong> <span id="structure-id"></span></p>
<p><strong>Number of atoms (Protein):</strong> <span id="atom-count"></span></p>
<p><strong>Chains:</strong> <span id="chain-info"></span></p>
<p><strong>Residues:</strong> <span id="residue-count"></span></p>
<p><strong>Water molecules:</strong> <span id="water-count"></span></p>
<p><strong>Ions:</strong> <span id="ion-count"></span></p>
<p><strong>Ligands:</strong> <span id="ligand-info"></span></p>
<p><strong>HETATM entries:</strong> <span id="hetatm-count"></span></p>
</div>
<div class="protein-visualization">
<div id="molecule-viewer" class="molecule-viewer">
<!-- 3D visualization will be added here -->
<div id="ngl-viewer" style="width: 100%; height: 100%; min-height: 300px;"></div>
<div id="viewer-controls" class="viewer-controls" style="display: none;">
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.resetView()">
<i class="fas fa-home"></i> Reset View
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleRepresentation()">
<i class="fas fa-eye"></i> <span id="style-text">Mixed View</span>
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleSpin()">
<i class="fas fa-sync"></i> Spin
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Fill Missing Residues Tab -->
<div id="fill-missing" class="tab-content">
<div class="card">
<h2><i class="fas fa-puzzle-piece"></i> Fill Missing Residues</h2>
<p class="card-description">
Detect missing residues in the experimental structure using RCSB annotations and complete them
with ESMFold. You can choose which chains to include in the completion.
</p>
<p class="form-text text-muted" style="margin-top: 6px; font-size: 0.9em;">
<i class="fas fa-book"></i> If you use this workflow in your research, please cite: <a href="https://esmatlas.com/about" target="_blank" rel="noopener noreferrer">ESM Atlas</a>
</p>
<div class="prep-sections">
<div class="prep-section">
<h3><i class="fas fa-search"></i> Detect Missing Residues</h3>
<button class="btn btn-primary" id="detect-missing-residues">
<i class="fas fa-search"></i> Analyze Missing Residues
</button>
<div id="missing-status" class="status-message" style="margin-top: 10px;"></div>
</div>
<div class="prep-section" id="missing-chains-section" style="display: none;">
<h3><i class="fas fa-link"></i> Select Chains for Completion</h3>
<p class="option-description">
Chains listed below have missing residues. Select which chains you want to rebuild with ESMFold.
</p>
<div id="missing-chains-list" class="multi-checkbox-group">
<!-- Missing chains checkboxes will be rendered here -->
</div>
<small class="form-help">
At least one chain must be selected to build a completed structure.
</small>
</div>
</div>
<div class="prep-section prep-section-fullwidth" id="trim-residues-section" style="display: none;">
<h3><i class="fas fa-cut"></i> Trim Residues from Edges (Optional)</h3>
<p class="option-description">
Optionally trim residues from the N-terminal and/or C-terminal edges of selected chains.
This only removes residues from the edges, not from loops in between.
</p>
<div class="trim-info-box" id="trim-info-box-content">
<i class="fas fa-info-circle"></i>
<strong>Note:</strong> Only missing residues at the <strong>N-terminal edge</strong> (beginning of sequence) and <strong>C-terminal edge</strong> (end of sequence) can be trimmed.
Missing residues in internal loops (discontinuities in the middle of the sequence) cannot be trimmed using this tool and will be filled by ESMFold.
</div>
<div id="trim-residues-list" class="trim-residues-container">
<!-- Trim controls for each chain will be rendered here -->
</div>
<button class="btn btn-secondary" id="apply-trim" style="margin-top: 15px;">
<i class="fas fa-check"></i> Apply Trimming
</button>
<div id="trim-status" class="status-message" style="margin-top: 10px; display: none;"></div>
</div>
<!-- Chain Minimization Option -->
<div class="prep-section" id="chain-minimization-section" style="display: none; margin-top: 20px; padding: 15px; background: #f8f9fa; border-radius: 5px; border: 1px solid #dee2e6;">
<h3><i class="fas fa-compress-arrows-alt"></i> Energy Minimization (Optional)</h3>
<div class="form-check" style="display: flex; align-items: center; gap: 10px; margin-top: 10px;">
<input class="form-check-input" type="checkbox" id="minimize-chains-checkbox" style="width: 20px; height: 20px; cursor: pointer;">
<label class="form-check-label" for="minimize-chains-checkbox" style="cursor: pointer; font-weight: 500; flex: 1;">
<strong>Energy minimize ESMFold-generated chains</strong>
</label>
</div>
<small class="form-text text-muted" style="display: block; margin-top: 8px; margin-left: 30px;">
<i class="fas fa-info-circle"></i> Recommended: Minimization resolve structural clashes
</small>
<div id="minimization-chains-list" style="display: none; margin-top: 15px; margin-left: 30px;">
<strong>Select chains to minimize:</strong>
<div id="minimization-chains-checkboxes" class="multi-checkbox-group" style="margin-top: 10px;">
<!-- Chain checkboxes will be populated here -->
</div>
</div>
</div>
<div class="prep-actions">
<button class="btn btn-primary" id="build-complete-structure" disabled>
<i class="fas fa-magic"></i> Build Completed Structure
</button>
<button class="btn btn-secondary" id="preview-completed-structure" disabled>
<i class="fas fa-eye"></i> Preview Completed Structure
</button>
<button class="btn btn-secondary" id="preview-superimposed-structure" disabled>
<i class="fas fa-layer-group"></i> View Superimposed Structures
</button>
<button class="btn btn-info" id="download-completed-structure" disabled>
<i class="fas fa-download"></i> Download Completed PDB
</button>
</div>
<div class="prep-status" id="missing-summary" style="display: none;">
<h3><i class="fas fa-info-circle"></i> Missing Residues Summary</h3>
<div class="status-content" id="missing-summary-content">
<!-- Missing residues summary will be displayed here -->
</div>
</div>
<div class="prep-actions" id="sequence-viewer-actions" style="display: none; margin-top: 1rem;">
<button class="btn btn-secondary" id="view-protein-sequences">
<i class="fas fa-dna"></i> View Protein Sequences
</button>
</div>
<div class="prepared-structure-preview" id="sequence-viewer-section" style="display: none;">
<h3><i class="fas fa-dna"></i> Protein Sequence Viewer</h3>
<p class="card-description" style="margin-bottom: 15px;">
View protein sequences for all chains. Chain colors match the structure visualization. Missing residues are shown in grey.
</p>
<div id="sequence-viewer-content" class="sequence-viewer-container">
<!-- Sequence viewer will be rendered here -->
</div>
</div>
<div class="prepared-structure-preview" id="completed-structure-preview" style="display: none;">
<h3><i class="fas fa-eye"></i> Structure Comparison Preview</h3>
<p class="card-description" style="margin-bottom: 15px;">
Compare the completed structure (right) with the original crystal structure (left) to see the added missing residues.
</p>
<div class="preview-content" style="display: flex; justify-content: center; width: 100%; padding: 0;">
<div class="structure-comparison-container" style="display: flex; gap: 20px; flex-direction: row; width: 100%; max-width: 1400px; align-items: flex-start; justify-content: center;">
<!-- Original Structure Viewer -->
<div class="comparison-viewer" style="flex: 0 1 48%; min-width: 450px; max-width: 48%;">
<h4 style="text-align: center; margin-bottom: 10px; font-size: 14px;">
<i class="fas fa-dna"></i> Original Crystal Structure
</h4>
<div id="original-molecule-viewer" class="molecule-viewer" style="border: 2px solid #007bff; border-radius: 5px; width: 100%; height: 500px; position: relative;">
<div id="original-ngl-viewer" style="width: 100%; height: 100%; position: absolute; top: 0; left: 0;"></div>
<div id="original-viewer-controls" class="viewer-controls" style="display: none; justify-content: center; position: relative; z-index: 10;">
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.resetOriginalView()">
<i class="fas fa-home"></i> Reset
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleOriginalRepresentation()">
<i class="fas fa-eye"></i> <span id="original-style-text">Mixed</span>
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleOriginalSpin()">
<i class="fas fa-sync"></i> Spin
</button>
</div>
</div>
</div>
<!-- Completed Structure Viewer -->
<div class="comparison-viewer" style="flex: 0 1 48%; min-width: 450px; max-width: 48%;">
<h4 style="text-align: center; margin-bottom: 10px; font-size: 14px;">
<i class="fas fa-puzzle-piece"></i> Completed Structure
</h4>
<div id="completed-molecule-viewer" class="molecule-viewer" style="border: 2px solid #28a745; border-radius: 5px; width: 100%; height: 500px; position: relative;">
<div id="completed-ngl-viewer" style="width: 100%; height: 100%; position: absolute; top: 0; left: 0;"></div>
<div id="completed-viewer-controls" class="viewer-controls" style="display: none; justify-content: center; position: relative; z-index: 10;">
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.resetCompletedView()">
<i class="fas fa-home"></i> Reset
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleCompletedRepresentation()">
<i class="fas fa-eye"></i> <span id="completed-style-text">Mixed</span>
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleCompletedSpin()">
<i class="fas fa-sync"></i> Spin
</button>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="prepared-structure-preview" id="superimposed-structure-preview" style="display: none;">
<h3><i class="fas fa-layer-group"></i> Superimposed Structure View</h3>
<p class="card-description" style="margin-bottom: 15px;">
View both the original crystal structure (original colors) and completed structure (different chain colors) superimposed in the same viewer to see which residues were filled.
</p>
<div class="preview-content" style="display: flex; justify-content: center; width: 100%; padding: 0;">
<div class="structure-comparison-container" style="width: 100%; max-width: 1400px;">
<!-- Superimposed Structure Viewer -->
<div class="comparison-viewer" style="width: 100%;">
<div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 10px;">
<div>
<span style="color: #007bff; font-weight: 600;"><i class="fas fa-dna"></i> Original Crystal Structure</span>
<span style="margin: 0 10px;">|</span>
<span style="color: #28a745; font-weight: 600;"><i class="fas fa-puzzle-piece"></i> Completed Structure</span>
</div>
</div>
<div id="superimposed-molecule-viewer" class="molecule-viewer" style="border: 2px solid #007bff; border-radius: 5px; width: 100%; height: 600px; position: relative;">
<div id="superimposed-ngl-viewer" style="width: 100%; height: 100%; position: absolute; top: 0; left: 0;"></div>
<div id="superimposed-viewer-controls" class="viewer-controls" style="display: none; gap: 10px;">
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.resetSuperimposedView()">
<i class="fas fa-home"></i> Reset
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleSuperimposedRepresentation()">
<i class="fas fa-eye"></i> <span id="superimposed-style-text">Cartoon</span>
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.toggleSuperimposedSpin()">
<i class="fas fa-sync"></i> Spin
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Structure Preparation Tab -->
<div id="structure-prep" class="tab-content">
<div class="card">
<h2><i class="fas fa-tools"></i> Structure Preparation for AMBER</h2>
<p class="card-description">Prepare the protein structure for AMBER force field generation by cleaning and modifying the PDB file.</p>
<div class="prep-sections">
<div class="prep-section">
<h3><i class="fas fa-trash"></i> Remove Components</h3>
<div class="prep-options">
<div class="prep-option">
<label class="checkbox-container">
<input type="checkbox" id="remove-water" checked disabled>
<span class="checkmark"></span>
Remove water molecules
</label>
<p class="option-description">Remove all water molecules (HOH, WAT, TIP3, etc.) from the structure</p>
</div>
<div class="prep-option">
<label class="checkbox-container">
<input type="checkbox" id="remove-ions" checked disabled>
<span class="checkmark"></span>
Remove ions
</label>
<p class="option-description">Remove all ions (Na+, Cl-, K+, Mg2+, etc.) from the structure</p>
</div>
<div class="prep-option">
<label class="checkbox-container">
<input type="checkbox" id="remove-hydrogens" checked disabled>
<span class="checkmark"></span>
Remove hydrogen atoms
</label>
<p class="option-description">Remove all hydrogen atoms from the protein structure</p>
</div>
</div>
</div>
<div class="prep-section">
<h3><i class="fas fa-plus-circle"></i> Add Capping Groups and Select Protein Chains</h3>
<div class="prep-options">
<div class="prep-option">
<label class="checkbox-container">
<input type="checkbox" id="add-nme" checked>
<span class="checkmark"></span>
Add NME group (C-terminal)
</label>
<p class="option-description">Add N-methyl amide (NME) group to C-terminal residues</p>
</div>
<div class="prep-option">
<label class="checkbox-container">
<input type="checkbox" id="add-ace" checked>
<span class="checkmark"></span>
Add ACE group (N-terminal)
</label>
<p class="option-description">Add acetyl (ACE) group to N-terminal residues</p>
</div>
<div class="form-group">
<label>Preserve Chains for FF Generation:</label>
<div id="chain-selection" class="multi-checkbox-group">
<!-- Chain checkboxes will be rendered here -->
</div>
<small class="form-help">Select one or more protein chains to include in preparation</small>
</div>
</div>
</div>
<div class="prep-section">
<h3><i class="fas fa-pills"></i> Ligand Handling</h3>
<div class="prep-options">
<div class="prep-option">
<label class="checkbox-container">
<input type="checkbox" id="preserve-ligands">
<span class="checkmark"></span>
Preserve ligands
</label>
<p class="option-description">Keep ligands in the structure and append them at the end</p>
</div>
<div class="prep-option">
<div class="checkbox-with-button">
<label class="checkbox-container">
<input type="checkbox" id="separate-ligands">
<span class="checkmark"></span>
Create separate ligand file
</label>
<button class="btn btn-sm btn-outline-primary" id="download-ligand" disabled>
<i class="fas fa-download"></i>
</button>
</div>
<p class="option-description">Extract ligands to a separate PDB file for individual processing</p>
</div>
<div class="form-group">
<label>Select Ligands to Preserve</label>
<div id="ligand-selection" class="multi-checkbox-group">
<!-- Ligand checkboxes will be rendered here -->
</div>
<small class="form-help">Tick ligands to include. Unselected ligands will be ignored.</small>
</div>
</div>
</div>
</div>
<div class="prep-actions">
<button class="btn btn-primary" id="prepare-structure">
<i class="fas fa-magic"></i> Prepare Structure
</button>
<button class="btn btn-secondary" id="preview-prepared">
<i class="fas fa-eye"></i> Preview Prepared Structure
</button>
<button class="btn btn-info" id="download-prepared">
<i class="fas fa-download"></i> Download Prepared PDB
</button>
</div>
<div class="prep-status" id="prep-status" style="display: none;">
<h3><i class="fas fa-info-circle"></i> Preparation Status</h3>
<div class="status-content" id="prep-status-content">
<!-- Status information will be displayed here -->
</div>
</div>
<div class="prepared-structure-preview" id="prepared-structure-preview" style="display: none;">
<h3><i class="fas fa-eye"></i> Prepared Structure Preview</h3>
<div class="preview-content">
<div class="structure-info">
<p><strong>Original atoms</strong> <span style="font-size:0.9em; color:#6c757d;">(protein without H, before capping):</span> <span id="original-atoms"></span></p>
<p><strong>Prepared atoms</strong> <span style="font-size:0.9em; color:#6c757d;">(protein without H, after capping):</span> <span id="prepared-atoms"></span></p>
<p><strong>Removed components:</strong> <span id="removed-components"></span></p>
<p><strong>Added capping groups:</strong> <span id="added-capping"></span></p>
<p><strong>Ligands preserved:</strong> <span id="preserved-ligands"></span></p>
</div>
<div class="structure-visualization">
<div id="prepared-molecule-viewer" class="molecule-viewer">
<div id="prepared-ngl-viewer" style="width: 100%; height: 100%; min-height: 300px;"></div>
<div id="prepared-viewer-controls" class="viewer-controls" style="display: none;">
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.resetPreparedView()">
<i class="fas fa-home"></i> Reset View
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.togglePreparedRepresentation()">
<i class="fas fa-eye"></i> <span id="prepared-style-text">Mixed View</span>
</button>
<button class="btn btn-sm btn-secondary" onclick="mdPipeline.togglePreparedSpin()">
<i class="fas fa-sync"></i> Spin
</button>
</div>
</div>
</div>
</div>
</div>
<!-- Docking Section (visible only when ligands are preserved and present) -->
<div class="card plumed-section-card" id="docking-section" style="display: none; margin-top: 20px;">
<h2 class="plumed-toggle-header" id="docking-toggle-header">
<i class="fas fa-vial"></i> Ligand Docking
<i class="fas fa-chevron-down toggle-icon" id="docking-toggle-icon"></i>
</h2>
<p class="section-description">
Configure docking for preserved ligands using AutoDock Vina and Meeko. Select which ligands to dock,
define the Vina bounding box with live visualization, then run docking and choose poses.
</p>
<div class="custom-plumed-section" id="docking-content-section">
<!-- Ligand Selection -->
<div class="form-group" style="margin-bottom: 20px;">
<label><i class="fas fa-pills"></i> Select Ligands to Dock</label>
<p class="option-description" style="margin-bottom: 10px;">
Choose which preserved ligands should be included in docking calculations.
</p>
<div id="docking-ligand-selection" class="multi-checkbox-group">
<!-- Ligand checkboxes will be rendered here -->
</div>
</div>
<!-- Collapsible: Docking Setup (Visualization + Box Dimensions) -->
<div class="docking-setup-collapsible" style="margin-top: 10px; border: 1px solid #dee2e6; border-radius: 8px; overflow: hidden;">
<div class="docking-setup-header" id="docking-setup-toggle" style="background: linear-gradient(135deg, #6f42c1 0%, #8e5dd4 100%); color: white; padding: 12px 15px; cursor: pointer; display: flex; justify-content: space-between; align-items: center;">
<span><i class="fas fa-cube"></i> Docking Search Space Setup</span>
<i class="fas fa-chevron-up" id="docking-setup-toggle-icon" style="transition: transform 0.3s ease;"></i>
</div>
<div class="docking-setup-content" id="docking-setup-content" style="padding: 15px; background: white;">
<!-- Docking Search Space Visualization -->
<div class="prepared-structure-preview" id="docking-structure-preview">
<h4 style="margin-top: 0;"><i class="fas fa-eye"></i> Search Space Visualization</h4>
<p class="card-description" style="margin-bottom: 10px;">
The protein–ligand system is shown below. For each selected ligand, a bounding box (10×10×10 Å by default)
represents the Vina search space. Adjust box dimensions below to update the visualization live.
</p>
<!-- NGL Viewer - Matching section 2 aspect ratio -->
<div id="docking-ngl-viewer" class="molecule-viewer" style="border: 2px solid #6f42c1; border-radius: 5px; width: 100%; max-width: 700px; height: 500px; position: relative; margin: 0 auto;">
<!-- Docking NGL visualization will be added here -->
</div>
</div>
<!-- Box Dimensions - Below Visualization -->
<div id="docking-box-controls" style="margin-top: 15px; background: #f8f9fa; padding: 15px; border-radius: 5px; border: 1px solid #dee2e6;">
<h5 style="margin-top: 0; margin-bottom: 15px;"><i class="fas fa-sliders-h"></i> Box Dimensions for Selected Ligands</h5>
<div id="docking-setup-list" style="display: flex; flex-wrap: wrap; gap: 15px;">
<!-- Per-ligand box controls will be rendered here in a horizontal layout -->
</div>
</div>
<div class="prep-actions" style="margin-top: 15px;">
<button class="btn btn-primary" id="run-docking">
<i class="fas fa-vial"></i> Run Docking with Above Settings
</button>
</div>
</div>
</div>
<div id="docking-status" class="status-message" style="display: none; margin-top: 10px;"></div>
<div id="docking-poses-container" style="display: none; margin-top: 20px;">
<h4><i class="fas fa-project-diagram"></i> Visualize Binding Poses</h4>
<p class="option-description">
Browse through docked poses for each ligand. Use the navigation arrows to view different binding modes.
Select your preferred pose for the simulation.
</p>
<!-- Ligand selector tabs -->
<div id="docking-ligand-tabs" class="docking-ligand-tabs">
<!-- Ligand tabs will be rendered here -->
</div>
<!-- 3D Viewer with pose navigation -->
<div class="docking-poses-viewer-wrapper">
<div id="docking-poses-viewer" class="docking-poses-viewer"></div>
<!-- Pose navigation controls overlay -->
<div class="pose-nav-controls">
<button type="button" class="pose-nav-btn pose-nav-prev" id="pose-prev-btn" title="Previous Pose">
<i class="fas fa-chevron-left"></i>
</button>
<div class="pose-info-display">
<div class="pose-mode-label" id="pose-mode-label">Original Ligand</div>
<div class="pose-energy-label" id="pose-energy-label"></div>
<div class="pose-color-legend">
<span><span class="legend-dot original"></span> Original (green)</span>
<span><span class="legend-dot docked"></span> Docked (coral)</span>
</div>
</div>
<button type="button" class="pose-nav-btn pose-nav-next" id="pose-next-btn" title="Next Pose">
<i class="fas fa-chevron-right"></i>
</button>
</div>
</div>
<!-- Pose selection summary -->
<div id="docking-poses-list" class="docking-poses-selection">
<!-- Radio buttons for final selection will be rendered here -->
</div>
<div class="prep-actions" style="margin-top: 15px;">
<button class="btn btn-success" id="apply-docking-poses">
<i class="fas fa-check"></i> Use Selected Pose
</button>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Simulation Parameters Tab -->
<div id="simulation-params" class="tab-content">
<div class="card">
<h2><i class="fas fa-sliders-h"></i> Simulation Parameters</h2>
<div class="params-grid">
<div class="param-section">
<h3><i class="fas fa-cube"></i> System Setup</h3>
<div class="form-group">
<label for="box-type">Box Type:</label>
<select id="box-type">
<option value="cuboid">Cuboid</option>
</select>
</div>
<div class="form-group">
<label for="box-size">
Distance (Å):
<i class="fas fa-info-circle"
style="color: #007bff; margin-left: 5px; cursor: help;"
data-toggle="tooltip"
data-placement="top"
data-html="true"
title="The minimum distance between any atom originally present in solute and the edge of the periodic box is given by the distance parameter.">
</i>
</label>
<input type="number" id="box-size" value="10" step="1" min="5">
</div>
</div>
<div class="param-section" id="ligand-forcefield-section" style="display: none;">
<h3><i class="fas fa-atom"></i> Ligand Force Field</h3>
<div class="form-group">
<label for="ligand-forcefield">Ligand Force Field:</label>
<select id="ligand-forcefield">
<option value="gaff2">gaff2</option>
<option value="gaff">gaff</option>
</select>
</div>
<div class="form-group">
<button type="button" class="btn btn-primary" onclick="mdPipeline.generateLigandFF(event)">
<i class="fas fa-cogs"></i> Generate FF for Ligand
</button>
</div>
</div>
<div class="param-section">
<h3><i class="fas fa-flask"></i> Force Field & Water Model</h3>
<div class="form-group">
<label for="force-field">Protein Force Field:</label>
<select id="force-field">
<option value="ff14SB">ff14SB</option>
<option value="ff19SB">ff19SB</option>
</select>
</div>
<div class="form-group">
<label for="water-model">Water Model:</label>
<select id="water-model">
<option value="tip3p">TIP3P</option>
<option value="spce">SPCE</option>
</select>
</div>
<div class="form-group">
<label for="add-ions">Add Ions:</label>
<div class="ion-controls">
<select id="add-ions">
<option value="None">None</option>
<option value="Na+">Na+</option>
<option value="Cl-">Cl-</option>
</select>
<button type="button" class="btn btn-sm btn-outline-primary" onclick="mdPipeline.calculateNetCharge(event)">
<i class="fas fa-calculator"></i> Net Charge
</button>
</div>
</div>
</div>
<div class="param-section">
<h3><i class="fas fa-thermometer-half"></i> Temperature & Pressure</h3>
<div class="form-group">
<label for="temperature">Temperature (K):</label>
<input type="number" id="temperature" value="300" step="5" min="200" max="400">
</div>
<div class="form-group">
<label for="pressure">Pressure (atm):</label>
<input type="number" id="pressure" value="1.0" step="0.1" min="0.1">
</div>
<div class="form-group">
<label for="coupling-type">Thermostat:</label>
<select id="coupling-type">
<option value="langevin">Langevin</option>
</select>
</div>
</div>
<div class="param-section">
<h3><i class="fas fa-clock"></i> Integration Parameters</h3>
<div class="form-group">
<label for="timestep">Time Step (ps):</label>
<input type="number" id="timestep" value="0.002" step="0.001" min="0.001" max="0.005">
</div>
<div class="form-group">
<label for="cutoff">Cutoff Distance (Ang):</label>
<input type="number" id="cutoff" value="10.0" step="1" min="8" max="20">
</div>
<div class="form-group">
<label for="electrostatic">Electrostatic:</label>
<select id="electrostatic">
<option value="pme">PME</option>
</select>
</div>
</div>
</div>
</div>
</div>
<!-- Simulation Steps Tab -->
<div id="simulation-steps" class="tab-content">
<div class="card">
<h2><i class="fas fa-list-ol"></i> Simulation Steps Configuration</h2>
<div class="steps-container">
<div class="step-item">
<div class="step-header">
<h3><i class="fas fa-lock"></i> Restrained Minimization</h3>
<label class="switch">
<input type="checkbox" id="enable-restrained-min" checked disabled>
<span class="slider"></span>
</label>
</div>
<div class="step-content" id="restrained-min-content">
<div class="form-row">
<div class="form-group">
<label for="restrained-steps">Steps:</label>
<input type="number" id="restrained-steps" value="10000" step="100" min="100">
</div>
<div class="form-group">
<label for="restrained-force">Force Constant (kJ/mol/Ų):</label>
<input type="number" id="restrained-force" value="10" step="1" min="1">
</div>
</div>
</div>
</div>
<div class="step-item">
<div class="step-header">
<h3><i class="fas fa-compress"></i> Minimization</h3>
<label class="switch">
<input type="checkbox" id="enable-minimization" checked disabled>
<span class="slider"></span>
</label>
</div>
<div class="step-content" id="minimization-content">
<div class="form-row">
<div class="form-group">
<label for="min-steps">Steps:</label>
<input type="number" id="min-steps" value="20000" step="500" min="1000">
</div>
<div class="form-group">
<label for="min-algorithm">Algorithm:</label>
<select id="min-algorithm">
<option value="cg">Conjugate Gradient</option>
</select>
</div>
</div>
</div>
</div>
<div class="step-item">
<div class="step-header">
<h3><i class="fas fa-fire"></i> NPT Heating</h3>
<label class="switch">
<input type="checkbox" id="enable-nvt" checked disabled>
<span class="slider"></span>
</label>
</div>
<div class="step-content" id="nvt-content">
<div class="form-row">
<div class="form-group">
<label for="nvt-steps">Steps:</label>
<input type="number" id="nvt-steps" value="50000" step="5000" min="10000">
</div>
<div class="form-group">
<label for="nvt-temp">Target Temperature (K):</label>
<input type="number" id="nvt-temp" value="300" step="5" min="200">
</div>
</div>
</div>
</div>
<div class="step-item">
<div class="step-header">
<h3><i class="fas fa-compress-arrows-alt"></i> NPT Equilibration</h3>
<label class="switch">
<input type="checkbox" id="enable-npt" checked disabled>
<span class="slider"></span>
</label>
</div>
<div class="step-content" id="npt-content">
<div class="form-row">
<div class="form-group">
<label for="npt-steps">Steps:</label>
<input type="number" id="npt-steps" value="100000" step="10000" min="20000">
</div>
<div class="form-group">
<label for="npt-temp">Temperature (K):</label>
<input type="number" id="npt-temp" value="300" step="5" min="200">
</div>
<div class="form-group">
<label for="npt-pressure">Pressure (atm):</label>
<input type="number" id="npt-pressure" value="1.0" step="0.1" min="0.1">
</div>
</div>
</div>
</div>
<div class="step-item">
<div class="step-header">
<h3><i class="fas fa-play"></i> Production Run(NPT)</h3>
<label class="switch">
<input type="checkbox" id="enable-production" checked disabled>
<span class="slider"></span>
</label>
</div>
<div class="step-content" id="production-content">
<div class="form-row">
<div class="form-group">
<label for="prod-steps">Steps:</label>
<input type="number" id="prod-steps" value="1000000" step="100000" min="100000">
</div>
<div class="form-group">
<label for="prod-temp">Temperature (K):</label>
<input type="number" id="prod-temp" value="300" step="5" min="200">
</div>
<div class="form-group">
<label for="prod-pressure">Pressure (atm):</label>
<input type="number" id="prod-pressure" value="1.0" step="0.1" min="0.1">
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<!-- File Generation Tab -->
<div id="file-generation" class="tab-content">
<!-- Guidance Note Card -->
<div class="plumed-citation-note">
<i class="fas fa-info-circle"></i>
<div class="citation-content">
<p>Click on <strong>Generate All Files</strong>. If you want to run <strong>biased simulations</strong> using PLUMED, proceed to the <strong>next section (PLUMED)</strong> to configure collective variables. Otherwise, download all files here and you're all set!</p>
</div>
</div>
<div class="card">
<h2><i class="fas fa-file-download"></i> Generate Simulation Files</h2>
<div class="generation-controls">
<button class="btn btn-primary" id="generate-files">
<i class="fas fa-magic"></i> Generate All Files
</button>
<button class="btn btn-secondary" id="preview-files">
<i class="fas fa-eye"></i> Preview Files
</button>
<button class="btn btn-info" id="preview-solvated">
<i class="fas fa-tint"></i> Preview Solvated Protein
</button>
<button class="btn btn-success" id="download-solvated">
<i class="fas fa-download"></i> Download Solvated Protein
</button>
</div>
<div class="files-preview" id="files-preview" style="display: none;">
<div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 15px;">
<h3 style="margin: 0;"><i class="fas fa-files"></i> Generated Files</h3>
<button class="btn btn-primary" id="add-simulation-file" style="margin-left: 10px;">
<i class="fas fa-plus"></i> Add Simulation File
</button>
</div>
<div class="files-list" id="files-list">
<!-- Generated files will be listed here -->
</div>
</div>
<div class="download-section" id="download-section" style="display: none;">
<h3><i class="fas fa-download"></i> Download Files</h3>
<div class="download-options">
<button class="btn btn-success" id="download-zip">
<i class="fas fa-file-archive"></i> Download All as ZIP
</button>
</div>
</div>
<div class="simulation-summary" id="simulation-summary" style="display: none;">
<h3><i class="fas fa-chart-line"></i> Simulation Summary</h3>
<div class="summary-content" id="summary-content">
<!-- Simulation summary will be displayed here -->
</div>
</div>
</div>
</div>
<!-- PLUMED Section -->
<div id="plumed" class="tab-content">
<!-- PLUMED Citation Note -->
<div class="plumed-citation-note">
<i class="fas fa-info-circle"></i>
<div class="citation-content">
<p><strong>Note:</strong> All CVs are taken from <a href="https://www.plumed.org/doc-v2.9/user-doc/html/index.html" target="_blank" rel="noopener noreferrer"><strong>PLUMED v2.9</strong> <i class="fas fa-external-link-alt"></i></a> documentation.</p>
<p>If you use PLUMED in your research, please cite it. <a href="https://www.plumed.org/cite" target="_blank" rel="noopener noreferrer">Citation information <i class="fas fa-external-link-alt"></i></a></p>
</div>
</div>
<!-- PLUMED Collective Variables Section -->
<div class="card plumed-section-card">
<h2>
<i class="fas fa-chart-line"></i> PLUMED Collective Variables
</h2>
<p class="section-description">
Configure Collective Variables (CVs) for biased MD simulations. Select a CV from the sidebar to view documentation and examples.
</p>
<div class="plumed-container" id="plumed-container">
<!-- Left Sidebar: CV List -->
<div class="plumed-sidebar">
<div class="sidebar-header">
<h3><i class="fas fa-list"></i> Collective Variables</h3>
<div class="search-box">
<input type="text" id="cv-search" placeholder="Search CVs..." class="search-input">
<i class="fas fa-search search-icon"></i>
</div>
</div>
<div class="cv-list" id="cv-list">
<!-- CV items will be populated by JavaScript -->
</div>
</div>
<!-- Right Panel: Documentation and Editor -->
<div class="plumed-content">
<div class="content-header" id="content-header" style="display: none;">
<h3 id="cv-title"></h3>
</div>
<div class="content-body" id="content-body">
<div class="welcome-message" id="welcome-message">
<i class="fas fa-hand-pointer fa-3x"></i>
<h3>Select a Collective Variable</h3>
<p>Choose a CV from the left sidebar to view its documentation and configure it for your simulation.</p>
</div>
<!-- Documentation Section -->
<div class="cv-documentation" id="cv-documentation" style="display: none;">
<div class="doc-section" id="cv-module-section" style="display: none;">
<h4><i class="fas fa-puzzle-piece"></i> Module</h4>
<div class="doc-content" id="cv-module"></div>
</div>
<div class="doc-section">
<h4><i class="fas fa-info-circle"></i> Description</h4>
<div class="doc-content" id="cv-description"></div>
</div>
<div class="doc-section">
<h4><i class="fas fa-code"></i> Syntax</h4>
<div class="doc-content">
<pre class="syntax-box" id="cv-syntax"></pre>
</div>
</div>
<div class="doc-section" id="cv-glossary-section" style="display: none;">
<h4><i class="fas fa-book"></i> Glossary of keywords and components</h4>
<div class="doc-content" id="cv-glossary"></div>
</div>
<div class="doc-section" id="cv-options-section" style="display: none;">
<h4><i class="fas fa-list-ul"></i> Options</h4>
<div class="doc-content" id="cv-options"></div>
</div>
<div class="doc-section" id="cv-components-section" style="display: none;">
<h4><i class="fas fa-cogs"></i> Components</h4>
<div class="doc-content" id="cv-components"></div>
</div>
<div class="doc-section">
<h4><i class="fas fa-book"></i> Examples</h4>
<div class="doc-content">
<pre class="example-box" id="cv-example"></pre>
</div>
</div>
<div class="doc-section" id="cv-notes-section" style="display: none;">
<h4><i class="fas fa-sticky-note"></i> Notes</h4>
<div class="doc-content" id="cv-notes"></div>
</div>
<div class="doc-section" id="cv-related-section" style="display: none;">
<h4><i class="fas fa-link"></i> Related Collective Variables</h4>
<div class="doc-content" id="cv-related"></div>
</div>
</div>
<!-- Editable Editor Section -->
<div class="cv-editor-section" id="cv-editor-section" style="display: none;">
<div class="editor-header">
<h4><i class="fas fa-edit"></i> Your Configuration</h4>
<div class="editor-actions">
<button class="btn btn-sm btn-info" id="copy-config">
<i class="fas fa-copy"></i> Copy
</button>
<button class="btn btn-sm btn-primary" id="view-pdb">
<i class="fas fa-eye"></i> View PDB
</button>
<button class="btn btn-sm btn-secondary" id="reset-cv">
<i class="fas fa-redo"></i> Reset to Example
</button>
<button class="btn btn-sm btn-success" id="save-config">
<i class="fas fa-save"></i> Save
</button>
</div>
</div>
<textarea id="cv-editor" class="cv-editor" placeholder="Enter your PLUMED configuration here..."></textarea>
<div class="editor-footer">
<span class="char-count"><span id="char-count">0</span> characters</span>
<span class="line-count"><span id="line-count">0</span> lines</span>
</div>
</div>
<!-- Saved Configurations -->
<div class="saved-configs" id="saved-configs" style="display: none;">
<h4><i class="fas fa-bookmark"></i> Saved Configurations</h4>
<div class="configs-list" id="configs-list">
<!-- Saved configs will be shown here -->
</div>
</div>
</div>
</div>
</div>
</div>
<!-- Custom PLUMED File Section -->
<div class="card plumed-section-card" id="custom-plumed-card">
<h2 class="plumed-toggle-header" id="custom-plumed-toggle-header">
<i class="fas fa-file-code"></i> Write Custom PLUMED File
<i class="fas fa-chevron-down toggle-icon" id="custom-plumed-toggle-icon"></i>
</h2>
<p class="section-description">
Write your custom PLUMED configuration from scratch. This editor allows you to create a complete PLUMED input file.
</p>
<div class="custom-plumed-section" id="custom-plumed-section">
<div class="custom-editor-header">
<h4><i class="fas fa-edit"></i> Custom PLUMED Configuration</h4>
<div class="editor-actions">
<button class="btn btn-sm btn-info" id="copy-custom-plumed">
<i class="fas fa-copy"></i> Copy
</button>
<button class="btn btn-sm btn-primary" id="view-pdb-custom">
<i class="fas fa-eye"></i> View PDB
</button>
<button class="btn btn-sm btn-success" id="download-custom-plumed">
<i class="fas fa-save"></i> Save
</button>
<button class="btn btn-sm btn-secondary" id="clear-custom-plumed">
<i class="fas fa-trash"></i> Clear
</button>
</div>
</div>
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