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<!DOCTYPE html>
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<title>MD Simulation Pipeline</title>
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<h1><i class="fas fa-atom"></i> MD Simulation Pipeline</h1>
<p>Molecular Dynamics Simulation Setup and File Generation</p>
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<!-- Navigation Tabs -->
<nav class="tab-navigation">
<button class="tab-button active" data-tab="protein-loading">
<i class="fas fa-upload"></i> Protein Loading
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<button class="tab-button" data-tab="structure-prep">
<i class="fas fa-tools"></i> Structure Preparation
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<button class="tab-button" data-tab="simulation-params">
<i class="fas fa-cogs"></i> Simulation Parameters
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<i class="fas fa-list-ol"></i> Simulation Steps
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<i class="fas fa-file-download"></i> Generate Files
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<!-- 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:</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>
<!-- 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>
<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>
<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>
<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 id="original-atoms"></span></p>
<p><strong>Prepared atoms:</strong> <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>
</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>
<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>
<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>
<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>
<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>
<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">
<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>
</div>
<div class="files-preview" id="files-preview" style="display: none;">
<h3><i class="fas fa-files"></i> Generated Files</h3>
<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>
</main>
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