css/styles.css

/* Reset and Base Styles */
* {
    margin: 0;
    padding: 0;
    box-sizing: border-box;
}

body {
    font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
    line-height: 1.6;
    color: #333;
    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
    min-height: 100vh;
}

.container {
    max-width: 1400px;
    margin: 0 auto;
    background: white;
    min-height: 100vh;
    box-shadow: 0 0 30px rgba(0, 0, 0, 0.1);
}

/* Header Styles */
.header {
    background: linear-gradient(135deg, #2c3e50 0%, #3498db 100%);
    color: white;
    padding: 2rem 0;
    text-align: center;
    box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
}

.header-content h1 {
    font-size: 2.5rem;
    margin-bottom: 0.5rem;
    font-weight: 300;
}

.header-content p {
    font-size: 1.1rem;
    opacity: 0.9;
}

.header i {
    margin-right: 0.5rem;
    color: #3498db;
}

/* Tab Navigation */
.tab-navigation {
    display: flex;
    background: #34495e;
    border-bottom: 3px solid #3498db;
    overflow-x: auto;
}

/* Step Navigation Controls */
.step-navigation {
    display: flex;
    justify-content: space-between;
    align-items: center;
    background: #ffffff;
    padding: 20px 30px;
    border-top: 1px solid #dee2e6;
    box-shadow: 0 -2px 8px rgba(0,0,0,0.1);
    position: sticky;
    bottom: 0;
    z-index: 100;
}

/* Checkbox with Button Layout */
.checkbox-with-button {
    display: flex;
    align-items: center;
    gap: 15px;
    margin-bottom: 10px;
}

.checkbox-with-button .checkbox-container {
    margin-bottom: 0;
    flex: 1;
}

.btn-sm {
    padding: 6px 12px;
    font-size: 12px;
    border-radius: 4px;
}

.btn-outline-primary {
    color: #007bff;
    border: 1px solid #007bff;
    background: transparent;
}

.btn-outline-primary:hover:not(:disabled) {
    color: white;
    background: #007bff;
    border-color: #007bff;
}

.btn-outline-primary:disabled {
    color: #6c757d;
    border-color: #6c757d;
    background: transparent;
    cursor: not-allowed;
}

.nav-btn {
    display: flex;
    align-items: center;
    gap: 8px;
    padding: 10px 20px;
    border: 2px solid #007bff;
    background: #007bff;
    color: white;
    border-radius: 25px;
    font-weight: 600;
    cursor: pointer;
    transition: all 0.3s ease;
    font-size: 14px;
}

.nav-btn:hover:not(:disabled) {
    background: #0056b3;
    border-color: #0056b3;
    transform: translateY(-2px);
    box-shadow: 0 4px 8px rgba(0,123,255,0.3);
}

.nav-btn:disabled {
    background: #6c757d;
    border-color: #6c757d;
    cursor: not-allowed;
    opacity: 0.6;
}

.step-indicator {
    display: flex;
    align-items: center;
    gap: 5px;
    font-weight: 600;
    color: #495057;
    font-size: 16px;
}

.step-indicator span {
    background: #e9ecef;
    padding: 8px 12px;
    border-radius: 20px;
    min-width: 30px;
    text-align: center;
}

.step-indicator #current-step {
    background: #007bff;
    color: white;
}

.tab-button {
    flex: 1;
    background: none;
    border: none;
    color: white;
    padding: 1rem 1.5rem;
    cursor: pointer;
    font-size: 1rem;
    font-weight: 500;
    transition: all 0.3s ease;
    border-bottom: 3px solid transparent;
    min-width: 200px;
}

.tab-button:hover {
    background: rgba(255, 255, 255, 0.1);
    transform: translateY(-2px);
}

.tab-button.active {
    background: #3498db;
    border-bottom-color: #e74c3c;
    transform: translateY(-2px);
}

.tab-button i {
    margin-right: 0.5rem;
    font-size: 1.1rem;
}

/* Main Content */
.main-content {
    padding: 2rem;
    min-height: 600px;
}

.tab-content {
    display: none;
    animation: fadeIn 0.5s ease-in-out;
}

.tab-content.active {
    display: block;
}

@keyframes fadeIn {
    from { opacity: 0; transform: translateY(20px); }
    to { opacity: 1; transform: translateY(0); }
}

/* Card Styles */
.card {
    background: white;
    border-radius: 12px;
    box-shadow: 0 8px 25px rgba(0, 0, 0, 0.1);
    padding: 2rem;
    margin-bottom: 2rem;
    border: 1px solid #e1e8ed;
}

.card h2 {
    color: #2c3e50;
    margin-bottom: 1.5rem;
    font-size: 1.8rem;
    font-weight: 600;
    border-bottom: 2px solid #3498db;
    padding-bottom: 0.5rem;
}

.card h2 i {
    margin-right: 0.5rem;
    color: #3498db;
}

/* Protein Loading Styles */
.input-methods {
    display: grid;
    grid-template-columns: 1fr auto 1fr;
    gap: 2rem;
    align-items: center;
    margin-bottom: 2rem;
}

.method-option {
    background: #f8f9fa;
    padding: 1.5rem;
    border-radius: 8px;
    border: 2px dashed #dee2e6;
    transition: all 0.3s ease;
}

.method-option:hover {
    border-color: #3498db;
    background: #f0f8ff;
}

.method-option h3 {
    color: #2c3e50;
    margin-bottom: 1rem;
    font-size: 1.2rem;
}

.method-option h3 i {
    margin-right: 0.5rem;
    color: #3498db;
}

.divider {
    text-align: center;
    font-weight: bold;
    color: #7f8c8d;
    font-size: 1.1rem;
}

.divider::before,
.divider::after {
    content: '';
    display: inline-block;
    width: 50px;
    height: 2px;
    background: #bdc3c7;
    vertical-align: middle;
    margin: 0 1rem;
}

/* File Upload Area */
.file-upload-area {
    border: 2px dashed #3498db;
    border-radius: 8px;
    padding: 2rem;
    text-align: center;
    cursor: pointer;
    transition: all 0.3s ease;
    background: #f8f9fa;
}

.file-upload-area:hover {
    background: #e3f2fd;
    border-color: #2980b9;
}

.file-upload-area i {
    font-size: 3rem;
    color: #3498db;
    margin-bottom: 1rem;
    display: block;
}

.file-upload-area p {
    margin-bottom: 1rem;
    color: #7f8c8d;
}

.file-info {
    background: #d4edda;
    border: 1px solid #c3e6cb;
    border-radius: 4px;
    padding: 1rem;
    margin-top: 1rem;
}

.file-info p {
    margin: 0.25rem 0;
    color: #155724;
}

/* PDB Fetch */
.pdb-fetch {
    margin-top: 1rem;
}

.input-group {
    display: flex;
    gap: 1rem;
    align-items: end;
}

.input-group label {
    font-weight: 600;
    color: #2c3e50;
    margin-bottom: 0.5rem;
    display: block;
}

.input-group input {
    flex: 1;
    padding: 0.75rem;
    border: 2px solid #dee2e6;
    border-radius: 4px;
    font-size: 1rem;
    transition: border-color 0.3s ease;
}

.input-group input:focus {
    outline: none;
    border-color: #3498db;
    box-shadow: 0 0 0 3px rgba(52, 152, 219, 0.1);
}

/* Status Messages */
.status-message {
    margin-top: 1rem;
    padding: 0.75rem;
    border-radius: 4px;
    font-weight: 500;
}

.status-message.success {
    background: #d4edda;
    color: #155724;
    border: 1px solid #c3e6cb;
}

.status-message.error {
    background: #f8d7da;
    color: #721c24;
    border: 1px solid #f5c6cb;
}

.status-message.info {
    background: #d1ecf1;
    color: #0c5460;
    border: 1px solid #bee5eb;
}

/* Protein Preview */
.protein-preview {
    margin-top: 2rem;
    background: #f8f9fa;
    border-radius: 8px;
    padding: 1.5rem;
    border: 1px solid #dee2e6;
}

.preview-content {
    display: grid;
    grid-template-columns: 1fr 1fr;
    gap: 2rem;
    margin-top: 1rem;
}

.protein-info p {
    margin: 0.5rem 0;
    font-size: 1rem;
}

.protein-visualization {
    background: white;
    border-radius: 4px;
    padding: 1rem;
    border: 1px solid #dee2e6;
    min-height: 300px;
    position: relative;
}

/* Ensure NGL viewer controls overlay within both original and prepared viewers */
.molecule-viewer {
    position: relative;
}

#ngl-viewer {
    border-radius: 4px;
    background: #f8f9fa;
    border: 1px solid #dee2e6;
}

.viewer-controls {
    position: absolute;
    top: 10px;
    right: 10px;
    display: flex;
    gap: 0.5rem;
    z-index: 10;
}

.viewer-controls .btn {
    padding: 0.25rem 0.5rem;
    font-size: 0.8rem;
    border-radius: 3px;
    box-shadow: 0 2px 4px rgba(0,0,0,0.1);
}

.viewer-controls .btn:hover {
    transform: translateY(-1px);
    box-shadow: 0 4px 8px rgba(0,0,0,0.15);
}

/* Simulation Parameters */
.params-grid {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
    gap: 2rem;
}

.param-section {
    background: #f8f9fa;
    padding: 1.5rem;
    border-radius: 8px;
    border: 1px solid #dee2e6;
}

.param-section h3 {
    color: #2c3e50;
    margin-bottom: 1rem;
    font-size: 1.2rem;
    border-bottom: 1px solid #bdc3c7;
    padding-bottom: 0.5rem;
}

.param-section h3 i {
    margin-right: 0.5rem;
    color: #3498db;
}

.form-group {
    margin-bottom: 1rem;
}

.form-group label {
    display: block;
    margin-bottom: 0.5rem;
    font-weight: 600;
    color: #2c3e50;
}

.form-group input,
.form-group select {
    width: 100%;
    padding: 0.75rem;
    border: 2px solid #dee2e6;
    border-radius: 4px;
    font-size: 1rem;
    transition: border-color 0.3s ease;
}

.form-group input:focus,
.form-group select:focus {
    outline: none;
    border-color: #3498db;
    box-shadow: 0 0 0 3px rgba(52, 152, 219, 0.1);
}

/* Simulation Steps */
.steps-container {
    display: flex;
    flex-direction: column;
    gap: 1.5rem;
}

.step-item {
    background: #f8f9fa;
    border-radius: 8px;
    border: 1px solid #dee2e6;
    overflow: hidden;
    transition: all 0.3s ease;
}

.step-item:hover {
    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.1);
    transform: translateY(-2px);
}

.step-header {
    display: flex;
    justify-content: space-between;
    align-items: center;
    padding: 1.5rem;
    background: #34495e;
    color: white;
    cursor: pointer;
}

.step-header h3 {
    margin: 0;
    font-size: 1.2rem;
    font-weight: 600;
}

.step-header h3 i {
    margin-right: 0.5rem;
    color: #3498db;
}

.step-content {
    padding: 1.5rem;
    background: white;
    display: none;
}

.step-content.active {
    display: block;
}

.form-row {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
    gap: 1rem;
}

/* Toggle Switch */
.switch {
    position: relative;
    display: inline-block;
    width: 60px;
    height: 34px;
}

.switch input {
    opacity: 0;
    width: 0;
    height: 0;
}

.slider {
    position: absolute;
    cursor: pointer;
    top: 0;
    left: 0;
    right: 0;
    bottom: 0;
    background-color: #ccc;
    transition: .4s;
    border-radius: 34px;
}

.slider:before {
    position: absolute;
    content: "";
    height: 26px;
    width: 26px;
    left: 4px;
    bottom: 4px;
    background-color: white;
    transition: .4s;
    border-radius: 50%;
}

input:checked + .slider {
    background-color: #3498db;
}

input:checked + .slider:before {
    transform: translateX(26px);
}

/* File Generation */
.generation-controls {
    display: flex;
    gap: 1rem;
    margin-bottom: 2rem;
    flex-wrap: wrap;
}

.files-preview {
    margin-bottom: 2rem;
}

.files-list {
    display: grid;
    grid-template-columns: repeat(auto-fill, minmax(300px, 1fr));
    gap: 1rem;
    margin-top: 1rem;
}

.file-item {
    background: #f8f9fa;
    border: 1px solid #dee2e6;
    border-radius: 8px;
    padding: 1rem;
    transition: all 0.3s ease;
}

.file-item:hover {
    background: #e3f2fd;
    border-color: #3498db;
    transform: translateY(-2px);
}

.file-item h4 {
    color: #2c3e50;
    margin-bottom: 0.5rem;
    font-size: 1.1rem;
}

.file-item p {
    color: #7f8c8d;
    font-size: 0.9rem;
    margin: 0.25rem 0;
}

.download-section {
    margin-bottom: 2rem;
}

.download-options {
    display: flex;
    gap: 1rem;
    flex-wrap: wrap;
    margin-top: 1rem;
}

.simulation-summary {
    background: #f8f9fa;
    border-radius: 8px;
    padding: 1.5rem;
    border: 1px solid #dee2e6;
}

.summary-content {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(250px, 1fr));
    gap: 1rem;
    margin-top: 1rem;
}

.summary-item {
    background: white;
    padding: 1rem;
    border-radius: 4px;
    border: 1px solid #dee2e6;
}

.summary-item h4 {
    color: #2c3e50;
    margin-bottom: 0.5rem;
    font-size: 1rem;
}

.summary-item p {
    color: #7f8c8d;
    margin: 0.25rem 0;
}

/* Checkbox Group Styles */
.checkbox-group {
    display: flex;
    gap: 1rem;
    margin-top: 0.5rem;
}

.checkbox-container {
    display: flex;
    align-items: center;
    cursor: pointer;
    font-size: 0.9rem;
    color: #495057;
}

.checkbox-container input[type="checkbox"] {
    margin-right: 0.5rem;
    transform: scale(1.2);
}

.checkbox-container:hover {
    color: #007bff;
}

/* Ion Controls */
.ion-controls {
    display: flex;
    gap: 0.5rem;
    align-items: center;
}

.ion-controls select {
    flex: 1;
}




#ligand-forcefield-section {
    transition: all 0.3s ease;
}

#ligand-forcefield-section.disabled {
    opacity: 0.5;
    pointer-events: none;
}

/* Tooltip styling for better text wrapping */
.tooltip {
    max-width: 300px;
}

.tooltip-inner {
    text-align: left;
    white-space: normal;
    word-wrap: break-word;
}

/* Button Styles */
.btn {
    display: inline-flex;
    align-items: center;
    padding: 0.75rem 1.5rem;
    border: none;
    border-radius: 6px;
    font-size: 1rem;
    font-weight: 600;
    cursor: pointer;
    transition: all 0.3s ease;
    text-decoration: none;
    gap: 0.5rem;
}

.btn:hover {
    transform: translateY(-2px);
    box-shadow: 0 4px 12px rgba(0, 0, 0, 0.15);
}

.btn:active {
    transform: translateY(0);
}

.btn-primary {
    background: linear-gradient(135deg, #3498db, #2980b9);
    color: white;
}

.btn-primary:hover {
    background: linear-gradient(135deg, #2980b9, #1f618d);
}

.btn-secondary {
    background: linear-gradient(135deg, #95a5a6, #7f8c8d);
    color: white;
}

.btn-secondary:hover {
    background: linear-gradient(135deg, #7f8c8d, #6c7b7d);
}

.btn-success {
    background: linear-gradient(135deg, #27ae60, #229954);
    color: white;
}

.btn-success:hover {
    background: linear-gradient(135deg, #229954, #1e8449);
}

.btn-info {
    background: linear-gradient(135deg, #17a2b8, #138496);
    color: white;
}

.btn-info:hover {
    background: linear-gradient(135deg, #138496, #117a8b);
}

.btn i {
    font-size: 1rem;
}

/* Footer */
.footer {
    background: #2c3e50;
    color: white;
    text-align: center;
    padding: 2rem;
    margin-top: 2rem;
}

.footer p {
    margin: 0;
    opacity: 0.8;
}

/* Responsive Design */
@media (max-width: 768px) {
    .container {
        margin: 0;
        box-shadow: none;
    }
    
    .header-content h1 {
        font-size: 2rem;
    }
    
    .tab-navigation {
        flex-direction: column;
    }
    
    .tab-button {
        min-width: auto;
        border-bottom: 1px solid #2c3e50;
    }
    
    .main-content {
        padding: 1rem;
    }
    
    .input-methods {
        grid-template-columns: 1fr;
    }
    
    .divider {
        order: 2;
    }
    
    .preview-content {
        grid-template-columns: 1fr;
    }
    
    .params-grid {
        grid-template-columns: 1fr;
    }
    
    .form-row {
        grid-template-columns: 1fr;
    }
    
    .generation-controls {
        flex-direction: column;
    }
    
    .download-options {
        flex-direction: column;
    }
    
    .summary-content {
        grid-template-columns: 1fr;
    }
}

@media (max-width: 480px) {
    .header-content h1 {
        font-size: 1.5rem;
    }
    
    .card {
        padding: 1rem;
    }
    
    .card h2 {
        font-size: 1.5rem;
    }
    
    .btn {
        padding: 0.5rem 1rem;
        font-size: 0.9rem;
    }
}

/* Loading Animation */
.loading {
    display: inline-block;
    width: 20px;
    height: 20px;
    border: 3px solid #f3f3f3;
    border-top: 3px solid #3498db;
    border-radius: 50%;
    animation: spin 1s linear infinite;
}

@keyframes spin {
    0% { transform: rotate(0deg); }
    100% { transform: rotate(360deg); }
}

/* Structure Preparation Styles */
.card-description {
    color: #7f8c8d;
    margin-bottom: 2rem;
    font-style: italic;
}

.prep-sections {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
    gap: 2rem;
    margin-bottom: 2rem;
}

.prep-section {
    background: #f8f9fa;
    border-radius: 8px;
    padding: 1.5rem;
    border: 1px solid #dee2e6;
}

.prep-section h3 {
    color: #2c3e50;
    margin-bottom: 1rem;
    font-size: 1.2rem;
    border-bottom: 1px solid #bdc3c7;
    padding-bottom: 0.5rem;
}

.prep-section h3 i {
    margin-right: 0.5rem;
    color: #3498db;
}

.prep-options {
    display: flex;
    flex-direction: column;
    gap: 1rem;
}

.prep-option {
    background: white;
    border-radius: 6px;
    padding: 1rem;
    border: 1px solid #e1e8ed;
    transition: all 0.3s ease;
}

.prep-option:hover {
    box-shadow: 0 2px 8px rgba(0, 0, 0, 0.1);
    transform: translateY(-1px);
}

.checkbox-container {
    display: flex;
    align-items: center;
    cursor: pointer;
    font-weight: 600;
    color: #2c3e50;
    margin-bottom: 0.5rem;
}

.checkbox-container input[type="checkbox"] {
    margin-right: 0.75rem;
    transform: scale(1.2);
}

.option-description {
    color: #7f8c8d;
    font-size: 0.9rem;
    margin: 0;
    margin-left: 1.5rem;
}

.prep-actions {
    display: flex;
    gap: 1rem;
    margin-bottom: 2rem;
    flex-wrap: wrap;
}

.prep-status {
    background: #e8f5e8;
    border: 1px solid #c3e6cb;
    border-radius: 8px;
    padding: 1.5rem;
    margin-bottom: 2rem;
}

.prep-status h3 {
    color: #155724;
    margin-bottom: 1rem;
}

.status-content {
    color: #155724;
}

.prepared-structure-preview {
    background: #f8f9fa;
    border-radius: 8px;
    padding: 1.5rem;
    border: 1px solid #dee2e6;
    margin-top: 2rem;
}

.prepared-structure-preview h3 {
    color: #2c3e50;
    margin-bottom: 1rem;
    font-size: 1.2rem;
}

.structure-info p {
    margin: 0.5rem 0;
    font-size: 1rem;
}

.structure-visualization {
    margin-top: 1rem;
}

#prepared-ngl-viewer {
    border-radius: 4px;
    background: #f8f9fa;
    border: 1px solid #dee2e6;
}

/* Custom Checkbox Styles */
.checkbox-container input[type="checkbox"] {
    appearance: none;
    width: 20px;
    height: 20px;
    border: 2px solid #bdc3c7;
    border-radius: 4px;
    background: white;
    position: relative;
    cursor: pointer;
    transition: all 0.3s ease;
}

.checkbox-container input[type="checkbox"]:checked {
    background: #3498db;
    border-color: #3498db;
}

.checkbox-container input[type="checkbox"]:checked::after {
    content: '✓';
    position: absolute;
    top: 50%;
    left: 50%;
    transform: translate(-50%, -50%);
    color: white;
    font-weight: bold;
    font-size: 14px;
}

.checkbox-container input[type="checkbox"]:hover {
    border-color: #3498db;
    box-shadow: 0 0 0 3px rgba(52, 152, 219, 0.1);
}

/* Responsive Design for Structure Prep */
@media (max-width: 768px) {
    .prep-sections {
        grid-template-columns: 1fr;
    }
    
    .prep-actions {
        flex-direction: column;
    }
    
    .prep-option {
        padding: 0.75rem;
    }
    
    .option-description {
        margin-left: 1.25rem;
    }
}

/* Utility Classes */
.text-center { text-align: center; }
.text-left { text-align: left; }
.text-right { text-align: right; }
.mt-1 { margin-top: 0.5rem; }
.mt-2 { margin-top: 1rem; }
.mt-3 { margin-top: 1.5rem; }
.mb-1 { margin-bottom: 0.5rem; }
.mb-2 { margin-bottom: 1rem; }
.mb-3 { margin-bottom: 1.5rem; }
.p-1 { padding: 0.5rem; }
.p-2 { padding: 1rem; }
.p-3 { padding: 1.5rem; }