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Update PDB viewers
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‎viewers/templates/PDB Viewer.html‎

Lines changed: 72 additions & 72 deletions
Original file line numberDiff line numberDiff line change
@@ -11,17 +11,17 @@
1111
<script type="importmap">
1212
{
1313
"imports": {
14-
"three": "https://cdn.jsdelivr.net/npm/three@0.174.0/build/three.module.min.js",
15-
"three/addons/": "https://cdn.jsdelivr.net/npm/three@0.174.0/examples/jsm/",
14+
"three": "https://cdn.jsdelivr.net/npm/three@0.178.0/build/three.module.min.js",
15+
"three/addons/": "https://cdn.jsdelivr.net/npm/three@0.178.0/examples/jsm/",
1616
"three-viewport-gizmo": "https://cdn.jsdelivr.net/npm/three-viewport-gizmo@1.0.1/dist/three-viewport-gizmo.min.js",
1717
"@monogrid/gainmap-js/decode": "https://cdn.jsdelivr.net/npm/@monogrid/gainmap-js@3.0.6/dist/decode.min.js",
1818
"@monogrid/gainmap-js/encode": "https://cdn.jsdelivr.net/npm/@monogrid/gainmap-js@3.0.6/dist/encode.min.js",
1919
"@monogrid/gainmap-js/libultrahdr": "https://cdn.jsdelivr.net/npm/@monogrid/gainmap-js@3.0.6/dist/libultrahdr.min.js",
2020
"@gltf-transform/core": "https://esm.sh/@gltf-transform/core@3.10.1",
2121
"@gltf-transform/extensions": "https://esm.sh/@gltf-transform/extensions@3.10.1",
2222
"@gltf-transform/functions": "https://esm.sh/@gltf-transform/functions@3.10.1",
23-
"meshoptimizer_encoder": "https://cdn.jsdelivr.net/npm/meshoptimizer@0.22.0/meshopt_encoder.module.min.js",
24-
"meshoptimizer_simplifier": "https://cdn.jsdelivr.net/npm/meshoptimizer@0.22.0/meshopt_simplifier.module.min.js"
23+
"meshoptimizer_encoder": "https://cdn.jsdelivr.net/npm/meshoptimizer@0.24.0/meshopt_encoder.module.min.js",
24+
"meshoptimizer_simplifier": "https://cdn.jsdelivr.net/npm/meshoptimizer@0.24.0/meshopt_simplifier.module.min.js"
2525
}
2626
}
2727
</script>
@@ -30,7 +30,7 @@
3030
<script src="https://cdn.jsdelivr.net/npm/jszip@3.10.1/dist/jszip.min.js" defer></script>
3131

3232
<!-- For encoding GLB exports with draco compression -->
33-
<script src="https://cdn.jsdelivr.net/npm/three@0.174.0/examples/jsm/libs/draco/draco_encoder.min.js" defer></script>
33+
<script src="https://cdn.jsdelivr.net/npm/three@0.178.0/examples/jsm/libs/draco/draco_encoder.min.js" defer></script>
3434

3535
<script>
3636
var THREE, manager, pdb_loader, pdb_obj, font_loader, label_font, isMobile, isNewiPad;
@@ -75,7 +75,7 @@
7575

7676
font_loader = new FontLoader( manager );
7777

78-
await font_loader.load( "https://cdn.jsdelivr.net/npm/three@0.174.0/examples/fonts/optimer_bold.typeface.json", function( font ) {
78+
await font_loader.load( "https://cdn.jsdelivr.net/npm/three@0.178.0/examples/fonts/optimer_bold.typeface.json", function( font ) {
7979
label_font = font;
8080
});
8181

@@ -347,7 +347,7 @@
347347

348348
<!-- mouse_wheel variable is used throughout as a trigger for rendering -->
349349

350-
<title>PDB Viewer (r174)</title>
350+
<title>PDB Viewer (r178)</title>
351351
</head>
352352
<body onload="reset_all(); document_ready(); disabled_changed();" onresize="resize();">
353353
<div id="fixed_menu" class="fixed-menu">
@@ -2560,7 +2560,7 @@
25602560
const { KTX2Loader } = await import( 'three/addons/loaders/KTX2Loader.min.js' );
25612561

25622562
ktx2_loader = new KTX2Loader( manager );
2563-
ktx2_loader.setTranscoderPath( 'https://cdn.jsdelivr.net/npm/three@0.174.0/examples/jsm/libs/basis/' );
2563+
ktx2_loader.setTranscoderPath( 'https://cdn.jsdelivr.net/npm/three@0.178.0/examples/jsm/libs/basis/' );
25642564
ktx2_loader.detectSupport( renderer );
25652565
manager.addHandler( /\.ktx2$/i, ktx2_loader );
25662566
}
@@ -2919,75 +2919,75 @@
29192919
'Ag': 'Atomic number: 47\nAtomic mass: 107.8682\nGroup 11: Transition metal (coinage)\nElectrons: 2, 8, 18, 18, 1',
29202920
'Cd': 'Atomic number: 48\nAtomic mass: 112.414\nGroup 12: Transition metal (Zinc Group)\nElectrons: 2, 8, 18, 18, 2',
29212921
'In': 'Atomic number: 49\nAtomic mass: 114.818\nGroup 13: Boron Group (other metal)\nElectrons: 2, 8, 18, 18, 3',
2922-
'Sn': 'Atomic number: 50\nAtomic mass: 118.71',
2923-
'Sb': 'Atomic number: 51\nAtomic mass: 121.76',
2924-
'Te': 'Atomic number: 52\nAtomic mass: 127.6',
2925-
'I': 'Atomic number: 53\nAtomic mass: 126.90447',
2926-
'Xe': 'Atomic number: 54\nAtomic mass: 131.293',
2927-
'Cs': 'Atomic number: 55\nAtomic mass: 132.9054',
2928-
'Ba': 'Atomic number: 56\nAtomic mass: 137.327',
2929-
'La': 'Atomic number: 57\nAtomic mass: 138.90547',
2930-
'Ce': 'Atomic number: 58\nAtomic mass: 140.116',
2931-
'Pr': 'Atomic number: 59\nAtomic mass: 140.90765',
2932-
'Nd': 'Atomic number: 60\nAtomic mass: 144.242',
2933-
'Pm': 'Atomic number: 61\nAtomic mass: 145',
2934-
'Sm': 'Atomic number: 62\nAtomic mass: 150.36',
2935-
'Eu': 'Atomic number: 63\nAtomic mass: 151.964',
2936-
'Gd': 'Atomic number: 64\nAtomic mass: 157.25',
2937-
'Tb': 'Atomic number: 65\nAtomic mass: 158.92535',
2938-
'Dy': 'Atomic number: 66\nAtomic mass: 162.5',
2939-
'Ho': 'Atomic number: 67\nAtomic mass: 164.93032',
2940-
'Er': 'Atomic number: 68\nAtomic mass: 167.259',
2941-
'Tm': 'Atomic number: 69\nAtomic mass: 168.93421',
2942-
'Yb': 'Atomic number: 70\nAtomic mass: 173.054',
2943-
'Lu': 'Atomic number: 71\nAtomic mass: 174.9668',
2944-
'Hf': 'Atomic number: 72\nAtomic mass: 178.49',
2945-
'Ta': 'Atomic number: 73\nAtomic mass: 180.94788',
2946-
'W': 'Atomic number: 74\nAtomic mass: 183.84',
2947-
'Re': 'Atomic number: 75\nAtomic mass: 186.207',
2922+
'Sn': 'Atomic number: 50\nAtomic mass: 118.71\nGroup 14: Carbon Group (tetrels)\nElectrons: 2, 8, 18, 18, 4',
2923+
'Sb': 'Atomic number: 51\nAtomic mass: 121.76\nGroup 15: Nitrogen Family (pnictogens)\nElectrons: 2, 8, 18, 18, 5',
2924+
'Te': 'Atomic number: 52\nAtomic mass: 127.60\nGroup 16: Oxygen Family (chalcogens)\nElectrons: 2, 8, 18, 18, 6',
2925+
'I': 'Atomic number: 53\nAtomic mass: 126.90447\nGroup 17: Halogens\nElectrons: 2, 8, 18, 18, 7',
2926+
'Xe': 'Atomic number: 54\nAtomic mass: 131.293\nGroup 18: Noble Gases\nElectrons: 2, 8, 18, 18, 8',
2927+
'Cs': 'Atomic number: 55\nAtomic mass: 132.90545196\nGroup 1: Alkali metal\nElectrons: 2, 8, 18, 18, 8, 1',
2928+
'Ba': 'Atomic number: 56\nAtomic mass: 137.327\nGroup 2: Alkaline earth metal\nElectrons: 2, 8, 18, 18, 8, 2',
2929+
'La': 'Atomic number: 57\nAtomic mass: 138.90547\nGroup 3: Lanthanides\nElectrons: 2, 8, 18, 18, 9, 2',
2930+
'Ce': 'Atomic number: 58\nAtomic mass: 140.116\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 19, 9, 2',
2931+
'Pr': 'Atomic number: 59\nAtomic mass: 140.90766\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 21, 8, 2',
2932+
'Nd': 'Atomic number: 60\nAtomic mass: 144.242\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 22, 8, 2',
2933+
'Pm': 'Atomic number: 61\nAtomic mass: 145\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 23, 8, 2',
2934+
'Sm': 'Atomic number: 62\nAtomic mass: 150.36\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 24, 8, 2',
2935+
'Eu': 'Atomic number: 63\nAtomic mass: 151.964\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 25, 8, 2',
2936+
'Gd': 'Atomic number: 64\nAtomic mass: 157.25\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 25, 9, 2',
2937+
'Tb': 'Atomic number: 65\nAtomic mass: 158.92535\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 27, 8, 2',
2938+
'Dy': 'Atomic number: 66\nAtomic mass: 162.500\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 28, 8, 2',
2939+
'Ho': 'Atomic number: 67\nAtomic mass: 164.93033\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 29, 8, 2',
2940+
'Er': 'Atomic number: 68\nAtomic mass: 167.259\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 30, 8, 2',
2941+
'Tm': 'Atomic number: 69\nAtomic mass: 168.93422\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 31, 8, 2',
2942+
'Yb': 'Atomic number: 70\nAtomic mass: 173.045\nGroup: Lanthanides (f-block)\nElectrons: 2, 8, 18, 32, 8, 2',
2943+
'Lu': 'Atomic number: 71\nAtomic mass: 174.9668\nGroup 3: Lanthanides\nElectrons: 2, 8, 18, 32, 9, 2',
2944+
'Hf': 'Atomic number: 72\nAtomic mass: 178.49\nGroup 4: Transition metal\nElectrons: 2, 8, 18, 32, 10, 2',
2945+
'Ta': 'Atomic number: 73\nAtomic mass: 180.94788\nGroup 5: Transition metal (Vanadium Group)\nElectrons: 2, 8, 18, 32, 11, 2',
2946+
'W': 'Atomic number: 74\nAtomic mass: 183.84\nGroup 6: Transition metal (refractory)\nElectrons: 2, 8, 18, 32, 12, 2',
2947+
'Re': 'Atomic number: 75\nAtomic mass: 186.207\nGroup 7: Manganese Group\nElectrons: 2, 8, 18, 32, 13, 2',
29482948
'Os': 'Atomic number: 76\nAtomic mass: 190.23\nGroup 8: Transition metal (Platinum Group)\nElectrons: 2, 8, 18, 32, 14, 2',
2949-
'Ir': 'Atomic number: 77\nAtomic mass: 192.217\nGroup 9: Transition metal (Platinum Group)\nElectrons: 2, 8, 18, 32, 15, 2',
2949+
'Ir': 'Atomic number: 77\nAtomic mass: 192.217\nGroup 9: Transition metal (rare)\nElectrons: 2, 8, 18, 32, 15, 2',
29502950
'Pt': 'Atomic number: 78\nAtomic mass: 195.084\nGroup 10: Transition metal (Platinum Group)\nElectrons: 2, 8, 18, 32, 17, 1',
29512951
'Au': 'Atomic number: 79\nAtomic mass: 196.966569\nGroup 11: Transition metal (coinage)\nElectrons: 2, 8, 18, 32, 18, 1',
2952-
'Hg': 'Atomic number: 80\nAtomic mass: 200.59\nGroup 12: Transition metal (Zinc Group)\nElectrons: 2, 8, 18, 32, 18, 2',
2953-
'Tl': 'Atomic number: 81\nAtomic mass: 204.3833\nGroup 13: Boron Group (other metal)\nElectrons: 2, 8, 18, 32, 18, 3',
2954-
'Pb': 'Atomic number: 82\nAtomic mass: 207.2',
2955-
'Bi': 'Atomic number: 83\nAtomic mass: 208.9804',
2956-
'Po': 'Atomic number: 84\nAtomic mass: 209',
2957-
'At': 'Atomic number: 85\nAtomic mass: 210',
2958-
'Rn': 'Atomic number: 86\nAtomic mass: 222',
2959-
'Fr': 'Atomic number: 87\nAtomic mass: 223',
2960-
'Ra': 'Atomic number: 88\nAtomic mass: 226',
2961-
'Ac': 'Atomic number: 89\nAtomic mass: 227',
2962-
'Th': 'Atomic number: 90\nAtomic mass: 232.03806',
2963-
'Pa': 'Atomic number: 91\nAtomic mass: 231.0588',
2964-
'U': 'Atomic number: 92\nAtomic mass: 238.02891',
2965-
'Np': 'Atomic number: 93\nAtomic mass: 237',
2966-
'Pu': 'Atomic number: 94\nAtomic mass: 244',
2967-
'Am': 'Atomic number: 95\nAtomic mass: 243',
2968-
'Cm': 'Atomic number: 96\nAtomic mass: 247',
2969-
'Bk': 'Atomic number: 97\nAtomic mass: 247',
2970-
'Cf': 'Atomic number: 98\nAtomic mass: 251',
2971-
'Es': 'Atomic number: 99\nAtomic mass: 252',
2972-
'Fm': 'Atomic number: 100\nAtomic mass: 257',
2973-
'Md': 'Atomic number: 101\nAtomic mass: 258',
2974-
'No': 'Atomic number: 102\nAtomic mass: 259',
2975-
'Lr': 'Atomic number: 103\nAtomic mass: 262',
2976-
'Rf': 'Atomic number: 104\nAtomic mass: 267',
2977-
'Db': 'Atomic number: 105\nAtomic mass: 268',
2978-
'Sg': 'Atomic number: 106\nAtomic mass: 267',
2979-
'Bh': 'Atomic number: 107\nAtomic mass: 270',
2980-
'Hs': 'Atomic number: 108\nAtomic mass: 271',
2981-
'Mt': 'Atomic number: 109\nAtomic mass: 276',
2982-
'Ds': 'Atomic number: 110\nAtomic mass: 281',
2983-
'Rg': 'Atomic number: 111\nAtomic mass: 282',
2952+
'Hg': 'Atomic number: 80\nAtomic mass: 200.592\nGroup 12: Transition metal (Zinc Group)\nElectrons: 2, 8, 18, 32, 18, 2',
2953+
'Tl': 'Atomic number: 81\nAtomic mass: 204.38\nGroup 13: Boron Group (other metal)\nElectrons: 2, 8, 18, 32, 18, 3',
2954+
'Pb': 'Atomic number: 82\nAtomic mass: 207.2\nGroup 14: Carbon Group (tetrels)\nElectrons: 2, 8, 18, 32, 18, 4',
2955+
'Bi': 'Atomic number: 83\nAtomic mass: 208.9804\nGroup 15: Nitrogen Family (pnictogens)\nElectrons: 2, 8, 18, 32, 18, 5',
2956+
'Po': 'Atomic number: 84\nAtomic mass: 209\nGroup 16: Oxygen Family (chalcogens)\nElectrons: 2, 8, 18, 32, 18, 6',
2957+
'At': 'Atomic number: 85\nAtomic mass: 210\nGroup 17: Halogens\nElectrons: 2, 8, 18, 32, 18, 7',
2958+
'Rn': 'Atomic number: 86\nAtomic mass: 222\nGroup 18: Noble Gases\nElectrons: 2, 8, 18, 32, 18, 8',
2959+
'Fr': 'Atomic number: 87\nAtomic mass: 223\nGroup 1: Alkali metal\nElectrons: 2, 8, 18, 32, 18, 8, 1',
2960+
'Ra': 'Atomic number: 88\nAtomic mass: 226\nGroup 2: Alkaline earth metal\nElectrons: 2, 8, 18, 32, 18, 8, 2',
2961+
'Ac': 'Atomic number: 89\nAtomic mass: 227\nGroup 3: Actinides\nElectrons: 2, 8, 18, 32, 18, 9, 2',
2962+
'Th': 'Atomic number: 90\nAtomic mass: 232.0377\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 18, 10, 2',
2963+
'Pa': 'Atomic number: 91\nAtomic mass: 231.03588\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 20, 9, 2',
2964+
'U': 'Atomic number: 92\nAtomic mass: 238.02891\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 21, 9, 2',
2965+
'Np': 'Atomic number: 93\nAtomic mass: 237\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 22, 9, 2',
2966+
'Pu': 'Atomic number: 94\nAtomic mass: 244\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 24, 8, 2',
2967+
'Am': 'Atomic number: 95\nAtomic mass: 243\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 25, 8, 2',
2968+
'Cm': 'Atomic number: 96\nAtomic mass: 247\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 25, 9, 2',
2969+
'Bk': 'Atomic number: 97\nAtomic mass: 247\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 27, 8, 2',
2970+
'Cf': 'Atomic number: 98\nAtomic mass: 251\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 28, 8, 2',
2971+
'Es': 'Atomic number: 99\nAtomic mass: 252\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 29, 8, 2',
2972+
'Fm': 'Atomic number: 100\nAtomic mass: 257\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 30, 8, 2',
2973+
'Md': 'Atomic number: 101\nAtomic mass: 258\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 31, 8, 2',
2974+
'No': 'Atomic number: 102\nAtomic mass: 259\nGroup: Actinides (f-block)\nElectrons: 2, 8, 18, 32, 32, 8, 2',
2975+
'Lr': 'Atomic number: 103\nAtomic mass: 262\nGroup 3: Actinides\nElectrons: 2, 8, 18, 32, 32, 9, 2',
2976+
'Rf': 'Atomic number: 104\nAtomic mass: 267\nGroup 4: Transition metal\nElectrons: 2, 8, 18, 32, 32, 10, 2',
2977+
'Db': 'Atomic number: 105\nAtomic mass: 268\nGroup 5: Vanadium Group\nElectrons: 2, 8, 18, 32, 32, 11, 2',
2978+
'Sg': 'Atomic number: 106\nAtomic mass: 271\nGroup 6: Transition metal (refractory)\nElectrons: 2, 8, 18, 32, 32, 12, 2',
2979+
'Bh': 'Atomic number: 107\nAtomic mass: 272\nGroup 7: Manganese Group\nElectrons: 2, 8, 18, 32, 32, 13, 2',
2980+
'Hs': 'Atomic number: 108\nAtomic mass: 277\nGroup 8: Transition metal (Platinum Group)\nElectrons: 2, 8, 18, 32, 32, 14, 2',
2981+
'Mt': 'Atomic number: 109\nAtomic mass: 278\nGroup 9: Transition metal (rare)\nElectrons: 2, 8, 18, 32, 32, 15, 2',
2982+
'Ds': 'Atomic number: 110\nAtomic mass: 281\nGroup 10: Transition metal (Platinum Group)\nElectrons: 2, 8, 18, 32, 32, 17, 1',
2983+
'Rg': 'Atomic number: 111\nAtomic mass: 282\nGroup 11: Transition metal (coinage)\nElectrons: 2, 8, 18, 32, 32, 18, 1',
29842984
'Cn': 'Atomic number: 112\nAtomic mass: 285\nGroup 12: Transition metal (Zinc Group)\nElectrons: 2, 8, 18, 32, 32, 18, 2',
29852985
'Nh': 'Atomic number: 113\nAtomic mass: 286\nGroup 13: Boron Group (other metal)\nElectrons: 2, 8, 18, 32, 32, 18, 3',
2986-
'Fl': 'Atomic number: 114\nAtomic mass: 289',
2987-
'Mc': 'Atomic number: 115\nAtomic mass: 290',
2988-
'Lv': 'Atomic number: 116\nAtomic mass: 293',
2989-
'Ts': 'Atomic number: 117\nAtomic mass: 294',
2990-
'Og': 'Atomic number: 118\nAtomic mass: 294',
2986+
'Fl': 'Atomic number: 114\nAtomic mass: 289\nGroup 14: Carbon Group (tetrels)\nElectrons: 2, 8, 18, 32, 32, 18, 4',
2987+
'Mc': 'Atomic number: 115\nAtomic mass: 290\nGroup 15: Nitrogen Family (pnictogens)\nElectrons: 2, 8, 18, 32, 32, 18, 5',
2988+
'Lv': 'Atomic number: 116\nAtomic mass: 293\nGroup 16: Oxygen Family (chalcogens)\nElectrons: 2, 8, 18, 32, 32, 18, 6',
2989+
'Ts': 'Atomic number: 117\nAtomic mass: 294\nGroup 17: Halogens\nElectrons: 2, 8, 18, 32, 32, 18, 7',
2990+
'Og': 'Atomic number: 118\nAtomic mass: 294\nGroup 18: Noble Gases\nElectrons: 2, 8, 18, 32, 32, 18, 8'
29912991
};
29922992

29932993
// Get atom related data

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