Spaces:
Sleeping
Sleeping
File size: 39,021 Bytes
8607410 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 | """
3D Visualization Module for RNA Structure Comparison
Uses py3Dmol for interactive molecular visualization
"""
import numpy as np
from pathlib import Path
from rmsd_utils import (
parse_residue_atoms,
translate_rotate_coords,
calculate_COM,
get_backbone_sugar_and_selectbase_coords_fixed
)
def create_structure_visualization(ref_path, query_path, ref_window_indices, query_window_indices,
rotation_matrix, ref_com, query_com, rmsd=None,
ref_name=None, query_name=None, ref_sequence=None, query_sequence=None):
"""
Create an interactive 3D visualization of aligned structures.
Args:
ref_path: Path to reference motif PDB file
query_path: Path to query motif PDB file
ref_window_indices: List of residue indices for the reference window
query_window_indices: List of residue indices for the query window
rotation_matrix: Rotation matrix from RMSD calculation
ref_com: Center of mass of reference window
query_com: Center of mass of query window
rmsd: RMSD value (optional, for display)
ref_name: Reference structure name (optional, for display)
query_name: Query structure name (optional, for display)
ref_sequence: Reference sequence (optional, for display)
query_sequence: Query sequence (optional, for display)
Returns:
HTML string containing the py3Dmol visualization
"""
# Extract simple names if not provided
if ref_name is None:
ref_name = Path(ref_path).stem
if query_name is None:
query_name = Path(query_path).stem
# Read PDB files
with open(ref_path) as f:
ref_pdb = f.read()
with open(query_path) as f:
query_pdb_full = f.read()
# Extract only the window residues from both structures
ref_residues = parse_residue_atoms(ref_path)
query_residues = parse_residue_atoms(query_path)
ref_window_pdb = extract_window_pdb(ref_path, ref_window_indices)
query_window_pdb = extract_window_pdb(query_path, query_window_indices)
# Parse window coordinates for transformation
from rmsd_utils import get_backbone_sugar_coords_from_residue, get_base_coords_from_residue
ref_window_coords = []
for idx in ref_window_indices:
if idx < len(ref_residues):
residue = ref_residues[idx]
backbone_coords = get_backbone_sugar_coords_from_residue(residue)
ref_window_coords.extend(backbone_coords)
base_coords = get_base_coords_from_residue(residue)
ref_window_coords.extend(base_coords)
ref_window_coords = np.asarray(ref_window_coords)
query_window_coords = []
for idx in query_window_indices:
if idx < len(query_residues):
residue = query_residues[idx]
backbone_coords = get_backbone_sugar_coords_from_residue(residue)
query_window_coords.extend(backbone_coords)
base_coords = get_base_coords_from_residue(residue)
query_window_coords.extend(base_coords)
query_window_coords = np.asarray(query_window_coords)
# Transform query window to align with reference window
# Proper alignment: translate to origin, rotate, translate to reference position
# Note: We need both query_com and ref_com for proper alignment
transformed_query_pdb = transform_pdb_string(
query_window_pdb,
rotation_matrix,
query_com,
ref_com # Add reference COM for proper alignment
)
# Create py3Dmol visualization
html = f"""
<!DOCTYPE html>
<html>
<head>
<script src="https://3Dmol.csb.pitt.edu/build/3Dmol-min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/html2canvas/1.4.1/html2canvas.min.js"></script>
<style>
#container {{
width: 100%;
height: 700px;
position: relative;
border: 1px solid #ddd;
}}
.control-panel {{
position: absolute;
top: 10px;
right: 10px;
background: rgba(255, 255, 255, 0.95);
padding: 15px;
border-radius: 8px;
font-family: Arial, sans-serif;
font-size: 13px;
z-index: 1000;
box-shadow: 0 2px 8px rgba(0,0,0,0.1);
max-width: 220px;
}}
.control-panel h4 {{
margin: 0 0 10px 0;
font-size: 14px;
color: #333;
}}
.control-section {{
margin-bottom: 12px;
padding-bottom: 12px;
border-bottom: 1px solid #eee;
}}
.control-section:last-child {{
border-bottom: none;
margin-bottom: 0;
}}
.control-section label {{
display: block;
margin: 6px 0;
cursor: pointer;
}}
.control-section input[type="checkbox"] {{
margin-right: 8px;
}}
.control-section select {{
width: 100%;
padding: 4px;
margin-top: 5px;
border: 1px solid #ccc;
border-radius: 4px;
}}
.legend {{
position: absolute;
top: 10px;
left: 10px;
background: rgba(255, 255, 255, 0.95);
padding: 15px;
border-radius: 8px;
font-family: Arial, sans-serif;
font-size: 13px;
z-index: 1000;
box-shadow: 0 2px 8px rgba(0,0,0,0.1);
}}
.legend h4 {{
margin: 0 0 10px 0;
font-size: 14px;
color: #333;
}}
.legend-item {{
margin: 6px 0;
display: flex;
align-items: center;
}}
.color-box {{
width: 24px;
height: 16px;
margin-right: 10px;
border: 1px solid #333;
border-radius: 2px;
}}
.rmsd-info {{
position: absolute;
bottom: 10px;
left: 10px;
background: rgba(255, 255, 255, 0.95);
padding: 12px 15px;
border-radius: 8px;
font-family: Arial, sans-serif;
font-size: 13px;
z-index: 1000;
box-shadow: 0 2px 8px rgba(0,0,0,0.1);
max-width: 450px;
}}
.info-row {{
margin: 4px 0;
line-height: 1.4;
}}
.info-label {{
font-weight: bold;
color: #555;
}}
.info-value {{
color: #333;
font-family: 'Courier New', monospace;
}}
.section-title {{
font-weight: bold;
color: #555;
margin-bottom: 5px;
font-size: 12px;
text-transform: uppercase;
}}
.download-section {{
position: absolute;
bottom: 10px;
right: 10px;
background: rgba(255, 255, 255, 0.95);
padding: 10px;
border-radius: 8px;
font-family: Arial, sans-serif;
z-index: 1000;
box-shadow: 0 2px 8px rgba(0,0,0,0.1);
}}
.download-btn {{
background: #4A90E2;
color: white;
border: none;
padding: 8px 16px;
border-radius: 4px;
cursor: pointer;
font-size: 13px;
font-weight: bold;
}}
.download-btn:hover {{
background: #357ABD;
}}
</style>
</head>
<body>
<div id="container"></div>
<div class="legend">
<h4>🧬 Structures</h4>
<div class="legend-item">
<div class="color-box" style="background: #4A90E2;"></div>
<span>Reference</span>
</div>
<div class="legend-item">
<div class="color-box" style="background: #E94B3C;"></div>
<span>Query (Aligned)</span>
</div>
</div>
<div class="control-panel">
<h4>⚙️ Display Options</h4>
<div class="control-section">
<div class="section-title">Structures</div>
<label>
<input type="checkbox" id="showRef" checked onchange="updateDisplay()">
Reference
</label>
<label>
<input type="checkbox" id="showQuery" checked onchange="updateDisplay()">
Query
</label>
</div>
<div class="control-section">
<div class="section-title">Style</div>
<select id="styleMode" onchange="updateDisplay()">
<option value="sticks">Sticks</option>
<option value="cartoon">Cartoon</option>
<option value="spheres">Spheres</option>
<option value="lines">Lines</option>
<option value="cartoon_sticks">Cartoon + Sticks</option>
</select>
</div>
<div class="control-section">
<div class="section-title">Components</div>
<label>
<input type="checkbox" id="showBackbone" checked onchange="updateDisplay()">
Backbone/Sugar
</label>
<label>
<input type="checkbox" id="showBases" checked onchange="updateDisplay()">
Bases
</label>
</div>
<div class="control-section">
<div class="section-title">Labels</div>
<label>
<input type="checkbox" id="showLabels" onchange="updateDisplay()">
Residue Labels
</label>
<label>
<input type="checkbox" id="showNumbers" onchange="updateDisplay()">
Residue Numbers
</label>
<label>
<input type="checkbox" id="showAtoms" onchange="updateDisplay()">
Atom Names
</label>
<select id="atomLabelMode" style="margin-top: 5px; font-size: 11px;" onchange="updateDisplay()">
<option value="all">All Atoms</option>
<option value="backbone">Backbone Only</option>
<option value="sidechain">Bases Only</option>
</select>
</div>
<div class="control-section">
<div class="section-title">Background</div>
<select id="bgColor" onchange="updateBackground()">
<option value="white">White</option>
<option value="black">Black</option>
<option value="gray">Gray</option>
</select>
</div>
<div class="control-section">
<div class="section-title">Annotation Font Size</div>
<select id="annotationFontSize">
<option value="small">Small (18pt/16pt/14pt)</option>
<option value="medium">Medium (22pt/18pt/16pt)</option>
<option value="large" selected>Large (28pt/22pt/18pt)</option>
<option value="xlarge">Extra Large (36pt/28pt/22pt)</option>
</select>
</div>
</div>
<div class="rmsd-info">
<div class="info-row">
<span class="info-label">RMSD:</span>
<span style="color: #E94B3C; font-weight: bold; font-size: 14px;">{f"{rmsd:.3f}" if rmsd is not None else "N/A"} Å</span>
</div>
<div style="margin-top: 8px; padding-top: 8px; border-top: 1px solid #ddd;">
<div class="info-row">
<span class="info-label">Reference:</span>
<span class="info-value">{ref_name}</span>
</div>
{f'<div class="info-row" style="margin-left: 15px; font-size: 12px;"><span class="info-label">Seq:</span> <span class="info-value">{ref_sequence}</span></div>' if ref_sequence else ''}
</div>
<div style="margin-top: 6px;">
<div class="info-row">
<span class="info-label">Query:</span>
<span class="info-value">{query_name}</span>
</div>
{f'<div class="info-row" style="margin-left: 15px; font-size: 12px;"><span class="info-label">Seq:</span> <span class="info-value">{query_sequence}</span></div>' if query_sequence else ''}
</div>
</div>
<div class="download-section">
<button class="download-btn" onclick="downloadImage()">📷 Download PNG</button>
</div>
<script>
let viewer = null;
let refModel = null;
let queryModel = null;
const refPDB = `{ref_window_pdb}`;
const queryPDB = `{transformed_query_pdb}`;
// RNA backbone atoms
const backboneAtoms = ['P', 'OP1', 'OP2', "O5'", "C5'", "C4'", "O4'", "C3'", "O3'", "C2'", "O2'", "C1'"];
function initViewer() {{
try {{
viewer = $3Dmol.createViewer("container", {{
backgroundColor: 'white'
}});
if (!refPDB || refPDB.length < 10) {{
throw new Error("Reference PDB data is empty");
}}
if (!queryPDB || queryPDB.length < 10) {{
throw new Error("Query PDB data is empty");
}}
updateDisplay();
viewer.zoomTo();
viewer.render();
}} catch (error) {{
console.error("Error initializing viewer:", error);
document.getElementById("container").innerHTML =
'<div style="padding: 20px; color: red; text-align: center;">Error loading visualization: ' + error.message + '</div>';
}}
}}
function updateBackground() {{
const bgColor = document.getElementById('bgColor').value;
viewer.setBackgroundColor(bgColor);
viewer.render();
}}
function updateDisplay() {{
if (!viewer) return;
try {{
// Clear everything
viewer.removeAllModels();
viewer.removeAllLabels();
const showRef = document.getElementById('showRef').checked;
const showQuery = document.getElementById('showQuery').checked;
const showBackbone = document.getElementById('showBackbone').checked;
const showBases = document.getElementById('showBases').checked;
const showLabels = document.getElementById('showLabels').checked;
const showNumbers = document.getElementById('showNumbers').checked;
const showAtoms = document.getElementById('showAtoms').checked;
const styleMode = document.getElementById('styleMode').value;
// Reference structure (blue)
if (showRef) {{
refModel = viewer.addModel(refPDB, "pdb");
applyStyle(refModel, '#4A90E2', '#5BA3F5', styleMode, showBackbone, showBases);
if (showLabels || showNumbers) {{
addResidueLabels(refModel, '#4A90E2', showLabels, showNumbers);
}}
if (showAtoms) {{
addAtomLabels(refModel, '#4A90E2');
}}
}}
// Query structure (red)
if (showQuery) {{
queryModel = viewer.addModel(queryPDB, "pdb");
applyStyle(queryModel, '#E94B3C', '#FF6B6B', styleMode, showBackbone, showBases);
if (showLabels || showNumbers) {{
addResidueLabels(queryModel, '#E94B3C', showLabels, showNumbers);
}}
if (showAtoms) {{
addAtomLabels(queryModel, '#E94B3C');
}}
}}
viewer.zoomTo();
viewer.render();
}} catch (error) {{
console.error("Error updating display:", error);
}}
}}
function applyStyle(model, backboneColor, baseColor, styleMode, showBackbone, showBases) {{
// Clear any existing styles
viewer.setStyle({{model: model}}, {{}});
if (styleMode === 'cartoon') {{
// Cartoon representation
viewer.setStyle({{model: model}}, {{
cartoon: {{
color: backboneColor,
thickness: 0.5,
opacity: 0.8
}}
}});
}} else if (styleMode === 'cartoon_sticks') {{
// Cartoon + sticks for bases
viewer.setStyle({{model: model}}, {{
cartoon: {{
color: backboneColor,
thickness: 0.5,
opacity: 0.7
}}
}});
if (showBases) {{
viewer.addStyle({{model: model, not: {{atom: backboneAtoms}}}}, {{
stick: {{
color: baseColor,
radius: 0.15
}}
}});
}}
}} else if (styleMode === 'spheres') {{
// Sphere representation
if (showBackbone) {{
viewer.setStyle({{model: model, atom: backboneAtoms}}, {{
sphere: {{
color: backboneColor,
radius: 0.4
}}
}});
}}
if (showBases) {{
viewer.addStyle({{model: model, not: {{atom: backboneAtoms}}}}, {{
sphere: {{
color: baseColor,
radius: 0.35
}}
}});
}}
}} else if (styleMode === 'lines') {{
// Line representation
if (showBackbone) {{
viewer.setStyle({{model: model, atom: backboneAtoms}}, {{
line: {{
color: backboneColor,
linewidth: 2
}}
}});
}}
if (showBases) {{
viewer.addStyle({{model: model, not: {{atom: backboneAtoms}}}}, {{
line: {{
color: baseColor,
linewidth: 2
}}
}});
}}
}} else {{
// Stick representation (default)
if (showBackbone) {{
viewer.setStyle({{model: model, atom: backboneAtoms}}, {{
stick: {{
color: backboneColor,
radius: 0.2
}},
sphere: {{
color: backboneColor,
radius: 0.3
}}
}});
}}
if (showBases) {{
viewer.addStyle({{model: model, not: {{atom: backboneAtoms}}}}, {{
stick: {{
color: baseColor,
radius: 0.15
}},
sphere: {{
color: baseColor,
radius: 0.25
}}
}});
}}
}}
}}
function addResidueLabels(model, color, showLabels, showNumbers) {{
const atoms = viewer.selectedAtoms({{model: model}});
const residues = {{}};
// Group atoms by residue
atoms.forEach(atom => {{
const key = atom.chain + '_' + atom.resi;
if (!residues[key]) {{
residues[key] = atom;
}}
}});
// Add labels for each residue
Object.values(residues).forEach(atom => {{
let labelText = '';
if (showLabels && showNumbers) {{
labelText = atom.resn + atom.resi;
}} else if (showLabels) {{
labelText = atom.resn;
}} else if (showNumbers) {{
labelText = atom.resi.toString();
}}
if (labelText) {{
viewer.addLabel(labelText, {{
position: atom,
backgroundColor: color,
backgroundOpacity: 0.7,
fontColor: 'white',
fontSize: 11,
fontWeight: 'bold',
showBackground: true,
borderRadius: 3
}});
}}
}});
}}
function addAtomLabels(model, color) {{
const atomLabelMode = document.getElementById('atomLabelMode').value;
const atoms = viewer.selectedAtoms({{model: model}});
// Filter atoms based on mode
let filteredAtoms = atoms;
if (atomLabelMode === 'backbone') {{
// Only backbone atoms
filteredAtoms = atoms.filter(atom => backboneAtoms.includes(atom.atom));
}} else if (atomLabelMode === 'sidechain') {{
// Only base/sidechain atoms (not backbone)
filteredAtoms = atoms.filter(atom => !backboneAtoms.includes(atom.atom));
}}
// 'all' mode uses all atoms (no filtering)
// Add label for each atom
filteredAtoms.forEach(atom => {{
// Use atom name (e.g., P, C1', N1, O4, etc.)
const atomName = atom.atom;
viewer.addLabel(atomName, {{
position: atom,
backgroundColor: color,
backgroundOpacity: 0.6,
fontColor: 'white',
fontSize: 9,
fontWeight: 'normal',
showBackground: true,
borderRadius: 2,
borderThickness: 0.5
}});
}});
}}
function downloadImage() {{
try {{
// Generate filename with metadata
var refName = "{ref_name}".replace('.pdb', '');
var queryName = "{query_name}".replace('.pdb', '');
var rmsdValue = "{f'{rmsd:.3f}' if rmsd is not None else 'NA'}";
var refSeq = "{ref_sequence if ref_sequence else ''}";
var querySeq = "{query_sequence if query_sequence else ''}";
var filenameOriginal = 'alignment_' + refName + '_' + queryName + '_RMSD_' + rmsdValue + '.png';
var filenameAnnotated = 'annotated_' + refName + '_' + queryName + '_RMSD_' + rmsdValue + '.png';
// Get selected font size
const fontSizeSelect = document.getElementById('annotationFontSize');
const fontSizeOption = fontSizeSelect ? fontSizeSelect.value : 'large';
// Define font sizes based on selection (all values are at 2x scale for high resolution)
let fontSizes;
switch(fontSizeOption) {{
case 'small':
fontSizes = {{ rmsd: 36, name: 32, seq: 28 }}; // 18pt/16pt/14pt at 2x
break;
case 'medium':
fontSizes = {{ rmsd: 44, name: 36, seq: 32 }}; // 22pt/18pt/16pt at 2x
break;
case 'large':
fontSizes = {{ rmsd: 56, name: 44, seq: 36 }}; // 28pt/22pt/18pt at 2x
break;
case 'xlarge':
fontSizes = {{ rmsd: 72, name: 56, seq: 44 }}; // 36pt/28pt/22pt at 2x
break;
default:
fontSizes = {{ rmsd: 56, name: 44, seq: 36 }}; // Default to large
}}
// Ensure viewer is rendered
if (viewer) {{
viewer.render();
}}
// Get the container element
const container = document.getElementById('container');
if (!container) {{
alert('Container not ready. Please wait and try again.');
return;
}}
// Use html2canvas to capture the entire container with overlays
html2canvas(container, {{
backgroundColor: '#ffffff',
scale: 2, // Higher resolution
logging: false,
useCORS: true,
allowTaint: true
}}).then(function(canvas) {{
// Create ANNOTATED version
const annotatedCanvas = document.createElement('canvas');
annotatedCanvas.width = canvas.width;
annotatedCanvas.height = canvas.height;
const ctx = annotatedCanvas.getContext('2d');
// Draw the original image onto new canvas
ctx.drawImage(canvas, 0, 0);
// Add annotations
const margin = 30; // Scaled for 2x resolution
const padding = 24;
const lineSpacing = 16;
// Prepare annotation text with selected font sizes
const annotations = [
{{ text: 'RMSD: ' + rmsdValue + ' Å', fontSize: fontSizes.rmsd, fontFamily: 'bold Arial', color: '#E94B3C' }},
{{ text: '', fontSize: 20, fontFamily: 'Arial', color: '#333' }}, // Spacer
{{ text: 'Reference: ' + refName, fontSize: fontSizes.name, fontFamily: 'Arial', color: '#333' }},
{{ text: ' Seq: ' + refSeq, fontSize: fontSizes.seq, fontFamily: 'Courier New, monospace', color: '#666' }},
{{ text: '', fontSize: 20, fontFamily: 'Arial', color: '#333' }}, // Spacer
{{ text: 'Query: ' + queryName, fontSize: fontSizes.name, fontFamily: 'Arial', color: '#333' }},
{{ text: ' Seq: ' + querySeq, fontSize: fontSizes.seq, fontFamily: 'Courier New, monospace', color: '#666' }}
];
// Calculate box dimensions
let maxWidth = 0;
let totalHeight = padding * 2;
const textMetrics = [];
annotations.forEach(ann => {{
if (ann.text) {{
ctx.font = ann.fontSize + 'px ' + ann.fontFamily;
const metrics = ctx.measureText(ann.text);
const height = ann.fontSize * 1.2; // Approximate height
textMetrics.push({{ width: metrics.width, height: height }});
maxWidth = Math.max(maxWidth, metrics.width);
totalHeight += height + lineSpacing;
}} else {{
textMetrics.push({{ width: 0, height: lineSpacing / 2 }});
totalHeight += lineSpacing / 2;
}}
}});
const boxWidth = maxWidth + padding * 2;
const boxHeight = totalHeight;
// Position box in bottom-left
const boxX = margin;
const boxY = annotatedCanvas.height - boxHeight - margin;
// Draw semi-transparent white background with rounded corners
ctx.fillStyle = 'rgba(255, 255, 255, 0.95)';
const radius = 16;
ctx.beginPath();
ctx.moveTo(boxX + radius, boxY);
ctx.lineTo(boxX + boxWidth - radius, boxY);
ctx.quadraticCurveTo(boxX + boxWidth, boxY, boxX + boxWidth, boxY + radius);
ctx.lineTo(boxX + boxWidth, boxY + boxHeight - radius);
ctx.quadraticCurveTo(boxX + boxWidth, boxY + boxHeight, boxX + boxWidth - radius, boxY + boxHeight);
ctx.lineTo(boxX + radius, boxY + boxHeight);
ctx.quadraticCurveTo(boxX, boxY + boxHeight, boxX, boxY + boxHeight - radius);
ctx.lineTo(boxX, boxY + radius);
ctx.quadraticCurveTo(boxX, boxY, boxX + radius, boxY);
ctx.closePath();
ctx.fill();
// Draw border
ctx.strokeStyle = 'rgba(200, 200, 200, 0.95)';
ctx.lineWidth = 2;
ctx.stroke();
// Draw text
let currentY = boxY + padding;
annotations.forEach((ann, idx) => {{
if (ann.text) {{
ctx.font = ann.fontSize + 'px ' + ann.fontFamily;
ctx.fillStyle = ann.color;
ctx.fillText(ann.text, boxX + padding, currentY + textMetrics[idx].height * 0.8);
currentY += textMetrics[idx].height + lineSpacing;
}} else {{
currentY += textMetrics[idx].height;
}}
}});
// Download ONLY the annotated PNG
const annotatedDataURL = annotatedCanvas.toDataURL('image/png');
const linkAnnotated = document.createElement('a');
linkAnnotated.download = filenameAnnotated;
linkAnnotated.href = annotatedDataURL;
document.body.appendChild(linkAnnotated);
linkAnnotated.click();
document.body.removeChild(linkAnnotated);
}}).catch(function(error) {{
console.error('html2canvas error:', error);
alert('Error creating images. Please try again.');
}});
}} catch (error) {{
console.error('PNG download error:', error);
alert('Error downloading PNG: ' + error.message);
}}
}}
// Initialize on load
initViewer();
</script>
</body>
</html>
"""
return html
def extract_window_pdb(pdb_path, window_indices):
"""
Extract specific residues from a PDB file based on window indices.
Args:
pdb_path: Path to PDB file
window_indices: List of residue indices (0-based)
Returns:
String containing PDB data for only the specified residues
"""
with open(pdb_path) as f:
lines = f.readlines()
# Get all residue numbers from the file
residues = parse_residue_atoms(pdb_path)
if not residues:
# If parsing failed, return original file
return ''.join(lines)
residue_numbers = [res['resnum'] for res in residues]
# Map window indices to actual residue numbers
target_resnums = set()
for idx in window_indices:
if idx < len(residue_numbers):
target_resnums.add(residue_numbers[idx])
if not target_resnums:
# If no valid residues, return original file
return ''.join(lines)
# Extract lines for these residues
window_lines = []
for line in lines:
if len(line) < 6:
continue
record = line[0:6].strip()
if record in ['ATOM', 'HETATM', 'HETAT']:
try:
# Handle different PDB formats
resnum_str = line[22:26].strip()
if resnum_str:
resnum = int(resnum_str)
if resnum in target_resnums:
window_lines.append(line)
except (ValueError, IndexError):
continue
elif record in ['HEADER', 'TITLE', 'MODEL', 'ENDMDL']:
window_lines.append(line)
# Always add END record
if window_lines and not any('END' in line for line in window_lines):
window_lines.append('END\n')
result = ''.join(window_lines)
# Debug: print info about extraction
if not result or len(result) < 50:
print(f"Warning: Empty or very small PDB extracted from {pdb_path}")
print(f" Window indices: {window_indices}")
print(f" Target residue numbers: {target_resnums}")
print(f" Result length: {len(result)}")
# Return full structure if extraction failed
return ''.join(lines)
return result
def transform_pdb_string(pdb_string, rotation_matrix, query_com, ref_com=None):
"""
Apply rotation and translation to coordinates in a PDB string to align with reference.
The transformation aligns the query structure to the reference structure:
1. Translate query to origin (subtract query_com)
2. Apply rotation matrix
3. Translate to reference position (add ref_com)
Args:
pdb_string: PDB format string
rotation_matrix: 3x3 rotation matrix
query_com: Center of mass of query structure (to translate FROM)
ref_com: Center of mass of reference structure (to translate TO), optional
Returns:
Transformed PDB string with aligned coordinates
"""
lines = pdb_string.split('\n')
transformed_lines = []
# If ref_com not provided, just center at origin after rotation
if ref_com is None:
ref_com = np.array([0.0, 0.0, 0.0])
for line in lines:
if len(line) < 54:
transformed_lines.append(line)
continue
record = line[0:6].strip()
if record in ['ATOM', 'HETATM', 'HETAT']:
# Extract coordinates
try:
x = float(line[30:38].strip())
y = float(line[38:46].strip())
z = float(line[46:54].strip())
# Transform: (coord - query_com) @ rotation_matrix + ref_com
# This aligns query to reference coordinate system
coord = np.array([x, y, z])
centered = coord - query_com # Move query to origin
rotated = np.dot(centered, rotation_matrix) # Rotate
new_coord = rotated + ref_com # Move to reference position
# Write transformed line
new_line = (
line[:30] +
f"{new_coord[0]:8.3f}" +
f"{new_coord[1]:8.3f}" +
f"{new_coord[2]:8.3f}" +
line[54:]
)
transformed_lines.append(new_line)
except (ValueError, IndexError):
transformed_lines.append(line)
else:
transformed_lines.append(line)
return '\n'.join(transformed_lines) |