SNi
Author: Dennis Svatunek
Date:
23.02.2024
Version:
1.0
License:
CC BY-NC
Description:
SNi
View Code
<script src="https://code.jquery.com/jquery-3.6.0.min.js"></script>
<script src="https://3Dmol.org/build/3Dmol-min.js"></script>
<div style="text-align: center;">
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<script>
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function adjustSquares() {
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var viewer;
function addBondBetweenAtoms(atomNum1, atomNum2) {
// Convert 1-based indexing to 0-based indexing
var index1 = atomNum1 - 1;
var index2 = atomNum2 - 1;
// Access the atoms from the viewer model
var atoms = viewer.getModel().atoms;
var atom1 = atoms[index1];
var atom2 = atoms[index2];
// Add each atom's index to the other's bonds array if not already present
if (!atom1.bonds.includes(index2)) {
atom1.bonds.push(index2);
}
if (!atom2.bonds.includes(index1)) {
atom2.bonds.push(index1);
}
// Add a bond order of 1 to each atom's bondOrder array
// Assuming the bondOrder array exists and its length matches the bonds array length
atom1.bondOrder.push(1);
atom2.bondOrder.push(1);
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viewer.render();
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viewer = $3Dmol.createViewer("D0410", {defaultcolors: $3Dmol.elementColors.Jmol});
var xyz = `21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.603860278894\nC -0.525 1.064 -0.260\nH -0.063 1.600 -1.118\nC -2.039 1.090 -0.401\nH -2.525 0.607 0.469\nH -2.389 2.138 -0.479\nH -2.334 0.543 -1.319\nC 0.090 -0.312 -0.144\nC 0.975 -0.775 -1.137\nC -0.218 -1.147 0.951\nC 1.537 -2.060 -1.047\nH 1.222 -0.121 -1.988\nC 0.351 -2.427 1.047\nH -0.899 -0.789 1.739\nC 1.227 -2.887 0.046\nH 2.225 -2.413 -1.831\nH 0.109 -3.070 1.906\nH 1.670 -3.892 0.121\nO -0.209 1.827 0.978\nS 0.951 2.987 0.800\nO 1.096 3.575 2.146\nCl -0.250 4.461 -0.481\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.595847066757\nC -0.559 1.059 -0.279\nH -0.111 1.602 -1.157\nC -2.077 1.083 -0.425\nH -2.564 0.596 0.440\nH -2.442 2.120 -0.520\nH -2.366 0.519 -1.347\nC 0.057 -0.300 -0.162\nC 0.972 -0.750 -1.134\nC -0.248 -1.134 0.941\nC 1.553 -2.023 -1.027\nH 1.222 -0.096 -1.988\nC 0.344 -2.396 1.054\nH -0.947 -0.785 1.718\nC 1.240 -2.847 0.067\nH 2.255 -2.368 -1.800\nH 0.102 -3.039 1.917\nH 1.697 -3.844 0.154\nO -0.139 1.793 1.044\nS 1.035 2.925 0.804\nO 1.275 3.494 2.138\nCl -0.299 4.389 -0.439\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.580070458051\nC -0.596 1.048 -0.313\nH -0.154 1.604 -1.191\nC -2.113 1.076 -0.448\nH -2.600 0.587 0.412\nH -2.491 2.103 -0.560\nH -2.394 0.495 -1.373\nC 0.026 -0.287 -0.179\nC 0.969 -0.726 -1.131\nC -0.278 -1.121 0.930\nC 1.567 -1.987 -1.008\nH 1.221 -0.072 -1.987\nC 0.337 -2.368 1.062\nH -0.992 -0.783 1.697\nC 1.253 -2.809 0.088\nH 2.284 -2.325 -1.770\nH 0.095 -3.009 1.926\nH 1.722 -3.798 0.187\nO -0.062 1.771 1.123\nS 1.110 2.859 0.805\nO 1.444 3.419 2.126\nCl -0.347 4.323 -0.396\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.562134195769\nC -0.636 1.037 -0.351\nH -0.195 1.605 -1.223\nC -2.149 1.068 -0.473\nH -2.635 0.578 0.386\nH -2.540 2.086 -0.600\nH -2.420 0.472 -1.399\nC -0.005 -0.273 -0.194\nC 0.966 -0.701 -1.129\nC -0.307 -1.110 0.918\nC 1.581 -1.951 -0.989\nH 1.220 -0.048 -1.985\nC 0.330 -2.340 1.070\nH -1.037 -0.780 1.675\nC 1.265 -2.772 0.109\nH 2.311 -2.282 -1.740\nH 0.088 -2.979 1.935\nH 1.747 -3.753 0.219\nO 0.021 1.749 1.208\nS 1.177 2.793 0.806\nO 1.612 3.343 2.107\nCl -0.394 4.258 -0.350\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.544432502342\nC -0.674 1.031 -0.387\nH -0.235 1.607 -1.253\nC -2.184 1.059 -0.499\nH -2.668 0.569 0.359\nH -2.588 2.068 -0.641\nH -2.445 0.449 -1.425\nC -0.034 -0.258 -0.208\nC 0.963 -0.676 -1.125\nC -0.337 -1.098 0.906\nC 1.594 -1.914 -0.969\nH 1.218 -0.024 -1.982\nC 0.322 -2.311 1.077\nH -1.081 -0.778 1.653\nC 1.277 -2.734 0.130\nH 2.338 -2.239 -1.709\nH 0.081 -2.950 1.944\nH 1.770 -3.707 0.251\nO 0.106 1.723 1.291\nS 1.238 2.726 0.808\nO 1.779 3.265 2.081\nCl -0.441 4.192 -0.301\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.528154357685\nC -0.712 1.030 -0.423\nH -0.274 1.608 -1.283\nC -2.218 1.050 -0.526\nH -2.701 0.561 0.332\nH -2.635 2.050 -0.682\nH -2.468 0.426 -1.451\nC -0.062 -0.242 -0.220\nC 0.959 -0.651 -1.122\nC -0.366 -1.087 0.894\nC 1.607 -1.877 -0.949\nH 1.216 0.000 -1.978\nC 0.314 -2.283 1.084\nH -1.123 -0.773 1.630\nC 1.288 -2.696 0.151\nH 2.364 -2.195 -1.678\nH 0.074 -2.919 1.953\nH 1.794 -3.660 0.284\nO 0.193 1.694 1.375\nS 1.292 2.657 0.812\nO 1.945 3.182 2.047\nCl -0.488 4.124 -0.251\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.515106132078\nC -0.749 1.033 -0.459\nH -0.312 1.608 -1.311\nC -2.251 1.040 -0.555\nH -2.733 0.553 0.305\nH -2.681 2.032 -0.723\nH -2.489 0.404 -1.476\nC -0.088 -0.225 -0.230\nC 0.955 -0.626 -1.118\nC -0.393 -1.075 0.882\nC 1.618 -1.840 -0.929\nH 1.214 0.024 -1.974\nC 0.306 -2.254 1.091\nH -1.163 -0.767 1.608\nC 1.299 -2.657 0.173\nH 2.390 -2.150 -1.646\nH 0.066 -2.889 1.961\nH 1.816 -3.613 0.317\nO 0.283 1.664 1.458\nS 1.339 2.589 0.822\nO 2.108 3.096 2.004\nCl -0.536 4.055 -0.198\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.506536364711\nC -0.786 1.042 -0.492\nH -0.348 1.609 -1.339\nC -2.283 1.029 -0.586\nH -2.764 0.545 0.277\nH -2.725 2.013 -0.764\nH -2.510 0.381 -1.501\nC -0.111 -0.207 -0.239\nC 0.951 -0.601 -1.113\nC -0.420 -1.062 0.871\nC 1.629 -1.802 -0.909\nH 1.212 0.049 -1.970\nC 0.297 -2.225 1.098\nH -1.201 -0.759 1.586\nC 1.309 -2.618 0.194\nH 2.414 -2.105 -1.615\nH 0.058 -2.858 1.969\nH 1.838 -3.566 0.350\nO 0.372 1.631 1.538\nS 1.381 2.520 0.838\nO 2.269 3.003 1.952\nCl -0.585 3.982 -0.145\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.502649283907\nC -0.821 1.054 -0.523\nH -0.383 1.611 -1.366\nC -2.314 1.017 -0.617\nH -2.794 0.536 0.250\nH -2.768 1.994 -0.806\nH -2.529 0.359 -1.526\nC -0.133 -0.188 -0.247\nC 0.947 -0.574 -1.108\nC -0.445 -1.047 0.860\nC 1.640 -1.763 -0.889\nH 1.209 0.074 -1.965\nC 0.288 -2.195 1.104\nH -1.237 -0.749 1.565\nC 1.318 -2.579 0.216\nH 2.438 -2.059 -1.582\nH 0.050 -2.827 1.977\nH 1.859 -3.518 0.383\nO 0.461 1.594 1.617\nS 1.420 2.453 0.860\nO 2.426 2.902 1.889\nCl -0.634 3.905 -0.091\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.503011318739\nC -0.856 1.068 -0.551\nH -0.416 1.613 -1.393\nC -2.345 1.006 -0.648\nH -2.824 0.528 0.222\nH -2.811 1.975 -0.848\nH -2.546 0.337 -1.552\nC -0.152 -0.168 -0.254\nC 0.943 -0.547 -1.103\nC -0.468 -1.030 0.850\nC 1.650 -1.724 -0.868\nH 1.207 0.100 -1.959\nC 0.280 -2.165 1.110\nH -1.270 -0.737 1.545\nC 1.327 -2.538 0.238\nH 2.462 -2.013 -1.549\nH 0.041 -2.795 1.985\nH 1.879 -3.468 0.417\nO 0.548 1.554 1.693\nS 1.457 2.389 0.888\nO 2.576 2.793 1.815\nCl -0.682 3.823 -0.035\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.507016315398\nC -0.888 1.083 -0.576\nH -0.448 1.617 -1.419\nC -2.374 0.993 -0.680\nH -2.852 0.519 0.193\nH -2.851 1.956 -0.890\nH -2.563 0.316 -1.576\nC -0.170 -0.148 -0.261\nC 0.940 -0.520 -1.097\nC -0.490 -1.011 0.841\nC 1.660 -1.685 -0.847\nH 1.204 0.126 -1.953\nC 0.271 -2.135 1.116\nH -1.302 -0.723 1.526\nC 1.335 -2.497 0.260\nH 2.484 -1.965 -1.516\nH 0.033 -2.763 1.992\nH 1.898 -3.418 0.450\nO 0.633 1.511 1.767\nS 1.493 2.328 0.919\nO 2.716 2.676 1.732\nCl -0.729 3.738 0.020\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.513962636751\nC -0.919 1.098 -0.599\nH -0.479 1.622 -1.444\nC -2.403 0.981 -0.712\nH -2.880 0.511 0.165\nH -2.891 1.937 -0.932\nH -2.578 0.294 -1.601\nC -0.187 -0.127 -0.267\nC 0.935 -0.491 -1.090\nC -0.510 -0.990 0.833\nC 1.669 -1.644 -0.826\nH 1.201 0.153 -1.947\nC 0.263 -2.104 1.122\nH -1.331 -0.706 1.508\nC 1.342 -2.455 0.282\nH 2.506 -1.917 -1.483\nH 0.023 -2.730 1.999\nH 1.917 -3.368 0.484\nO 0.718 1.465 1.839\nS 1.532 2.270 0.951\nO 2.844 2.553 1.642\nCl -0.773 3.647 0.076\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.523014894634\nC -0.949 1.115 -0.619\nH -0.509 1.628 -1.469\nC -2.430 0.969 -0.743\nH -2.907 0.502 0.136\nH -2.929 1.918 -0.974\nH -2.593 0.273 -1.625\nC -0.202 -0.107 -0.272\nC 0.931 -0.462 -1.084\nC -0.529 -0.967 0.825\nC 1.678 -1.603 -0.804\nH 1.198 0.182 -1.941\nC 0.255 -2.073 1.128\nH -1.359 -0.688 1.490\nC 1.348 -2.413 0.305\nH 2.527 -1.867 -1.449\nH 0.014 -2.697 2.005\nH 1.935 -3.315 0.519\nO 0.804 1.415 1.908\nS 1.575 2.212 0.984\nO 2.958 2.426 1.548\nCl -0.816 3.552 0.133\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.533345400109\nC -0.978 1.132 -0.638\nH -0.538 1.635 -1.493\nC -2.458 0.956 -0.775\nH -2.934 0.493 0.107\nH -2.967 1.898 -1.016\nH -2.606 0.252 -1.650\nC -0.217 -0.086 -0.278\nC 0.926 -0.432 -1.076\nC -0.547 -0.943 0.818\nC 1.686 -1.561 -0.782\nH 1.195 0.211 -1.934\nC 0.247 -2.041 1.134\nH -1.386 -0.669 1.474\nC 1.354 -2.369 0.327\nH 2.548 -1.816 -1.415\nH 0.004 -2.662 2.012\nH 1.953 -3.262 0.553\nO 0.892 1.362 1.974\nS 1.625 2.152 1.015\nO 3.059 2.295 1.452\nCl -0.856 3.453 0.191\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.544390193605\nC -1.007 1.148 -0.655\nH -0.568 1.644 -1.516\nC -2.485 0.944 -0.807\nH -2.960 0.484 0.079\nH -3.004 1.879 -1.057\nH -2.620 0.232 -1.674\nC -0.231 -0.064 -0.283\nC 0.920 -0.401 -1.069\nC -0.563 -0.917 0.812\nC 1.694 -1.519 -0.760\nH 1.191 0.241 -1.927\nC 0.239 -2.007 1.140\nH -1.412 -0.648 1.459\nC 1.360 -2.325 0.349\nH 2.567 -1.764 -1.381\nH -0.006 -2.627 2.019\nH 1.969 -3.207 0.588\nO 0.980 1.307 2.035\nS 1.681 2.089 1.044\nO 3.149 2.164 1.358\nCl -0.895 3.348 0.247\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.555854339968\nC -1.036 1.165 -0.671\nH -0.597 1.653 -1.538\nC -2.512 0.931 -0.838\nH -2.986 0.475 0.050\nH -3.040 1.859 -1.098\nH -2.633 0.211 -1.697\nC -0.245 -0.042 -0.288\nC 0.914 -0.369 -1.061\nC -0.579 -0.889 0.807\nC 1.701 -1.476 -0.737\nH 1.186 0.272 -1.920\nC 0.231 -1.973 1.146\nH -1.437 -0.627 1.444\nC 1.366 -2.280 0.371\nH 2.586 -1.711 -1.347\nH -0.016 -2.591 2.026\nH 1.986 -3.152 0.624\nO 1.070 1.250 2.091\nS 1.743 2.021 1.069\nO 3.230 2.034 1.269\nCl -0.932 3.239 0.300\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.567468599680\nC -1.065 1.182 -0.686\nH -0.626 1.663 -1.560\nC -2.538 0.918 -0.869\nH -3.012 0.465 0.022\nH -3.076 1.839 -1.138\nH -2.646 0.191 -1.720\nC -0.259 -0.019 -0.292\nC 0.908 -0.336 -1.053\nC -0.594 -0.861 0.802\nC 1.707 -1.432 -0.715\nH 1.181 0.303 -1.912\nC 0.224 -1.938 1.153\nH -1.462 -0.606 1.429\nC 1.371 -2.234 0.393\nH 2.603 -1.657 -1.312\nH -0.026 -2.555 2.033\nH 2.001 -3.095 0.659\nO 1.161 1.192 2.142\nS 1.810 1.947 1.089\nO 3.304 1.906 1.186\nCl -0.968 3.125 0.351\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.578764742608\nC -1.094 1.196 -0.700\nH -0.655 1.674 -1.580\nC -2.564 0.905 -0.899\nH -3.038 0.456 -0.006\nH -3.112 1.820 -1.177\nH -2.658 0.171 -1.742\nC -0.272 0.004 -0.297\nC 0.903 -0.302 -1.045\nC -0.608 -0.832 0.799\nC 1.713 -1.387 -0.693\nH 1.176 0.336 -1.904\nC 0.217 -1.901 1.161\nH -1.487 -0.586 1.413\nC 1.376 -2.187 0.415\nH 2.620 -1.602 -1.279\nH -0.035 -2.518 2.040\nH 2.016 -3.037 0.694\nO 1.252 1.134 2.190\nS 1.881 1.869 1.105\nO 3.373 1.778 1.110\nCl -1.004 3.010 0.398\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.589096587674\nC -1.124 1.209 -0.714\nH -0.685 1.685 -1.599\nC -2.590 0.892 -0.929\nH -3.063 0.446 -0.033\nH -3.147 1.800 -1.216\nH -2.671 0.152 -1.764\nC -0.285 0.027 -0.301\nC 0.898 -0.266 -1.035\nC -0.621 -0.803 0.795\nC 1.719 -1.342 -0.671\nH 1.171 0.371 -1.895\nC 0.211 -1.864 1.169\nH -1.512 -0.567 1.398\nC 1.381 -2.140 0.436\nH 2.635 -1.546 -1.245\nH -0.044 -2.480 2.047\nH 2.030 -2.979 0.729\nO 1.343 1.075 2.234\nS 1.955 1.786 1.115\nO 3.440 1.650 1.039\nCl -1.040 2.895 0.440\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.597767592366\nC -1.154 1.220 -0.726\nH -0.714 1.698 -1.616\nC -2.616 0.879 -0.958\nH -3.088 0.437 -0.059\nH -3.182 1.780 -1.253\nH -2.683 0.134 -1.785\nC -0.299 0.050 -0.306\nC 0.893 -0.230 -1.024\nC -0.635 -0.774 0.792\nC 1.725 -1.296 -0.649\nH 1.166 0.406 -1.885\nC 0.205 -1.826 1.177\nH -1.537 -0.550 1.382\nC 1.386 -2.092 0.458\nH 2.650 -1.490 -1.212\nH -0.053 -2.441 2.054\nH 2.043 -2.921 0.763\nO 1.434 1.016 2.275\nS 2.031 1.699 1.122\nO 3.504 1.521 0.973\nCl -1.077 2.780 0.478\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.603948853761\nC -1.184 1.228 -0.739\nH -0.744 1.710 -1.632\nC -2.641 0.867 -0.986\nH -3.113 0.428 -0.085\nH -3.217 1.760 -1.290\nH -2.694 0.116 -1.805\nC -0.312 0.072 -0.311\nC 0.889 -0.192 -1.013\nC -0.648 -0.746 0.789\nC 1.731 -1.249 -0.626\nH 1.161 0.443 -1.873\nC 0.200 -1.787 1.186\nH -1.562 -0.534 1.365\nC 1.391 -2.043 0.480\nH 2.664 -1.434 -1.178\nH -0.061 -2.402 2.062\nH 2.056 -2.862 0.797\nO 1.526 0.956 2.313\nS 2.109 1.608 1.125\nO 3.566 1.392 0.910\nCl -1.116 2.668 0.512\n21\nCoordinates from ORCA-job .\NEB_MEP_ALL E -1318.606613064214\nC -1.215 1.231 -0.757\nH -0.774 1.722 -1.645\nC -2.666 0.854 -1.013\nH -3.139 0.418 -0.111\nH -3.252 1.740 -1.327\nH -2.705 0.099 -1.825\nC -0.326 0.094 -0.316\nC 0.886 -0.151 -1.000\nC -0.663 -0.717 0.785\nC 1.737 -1.201 -0.602\nH 1.157 0.482 -1.861\nC 0.196 -1.747 1.196\nH -1.588 -0.520 1.348\nC 1.397 -1.994 0.503\nH 2.678 -1.376 -1.145\nH -0.069 -2.362 2.070\nH 2.068 -2.802 0.832\nO 1.621 0.893 2.353\nS 2.185 1.516 1.121\nO 3.628 1.258 0.851\nCl -1.156 2.562 0.545\n`;
viewer.addModelsAsFrames(xyz, "xyz");
viewer.setStyle({}, {stick: {radius: 0.15}, sphere: {scale: 0.25}});
viewer.zoomTo({x: 0, y: 0, z: 0});
viewer.setView([-4.76190474723872e-8,2.114710523095536e-17,4.7619047646850815e-8,121.64359090191145,-0.4013241580632666,-0.7883743450570798,-0.3327179917373977,0.32665509361536543]);
viewer.zoom(1.0);
viewer.setBackgroundColor('#f9f9f9');
viewer.rotate(0, {x: 0, y: 1, z: 0});
viewer.setViewStyle({style: 'outline', color: 'black', width: 0.02});
console.log(viewer)
console.log(viewer.getModel().atoms[19]);
addBondBetweenAtoms(19, 21);
$("#D0410").css("position", "relative");
// Dynamically set the max slider value based on the number of frames
var frameCount = viewer.getModel().getNumFrames();
$('#D0410_slider').attr('max', frameCount - 1);
var framesToAddBonds = [1, 2, 3, 4, 5];
var framesWithAddedBonds = new Set();
function updateFrame(sliderValue) {
var frameIndex = parseInt(sliderValue);
viewer.setFrame(parseInt(frameIndex));
if (framesToAddBonds.includes(frameIndex) && !framesWithAddedBonds.has(frameIndex)) {
addBondBetweenAtoms(19, 21);
framesWithAddedBonds.add(frameIndex);
}
viewer.render();
}
$('#D0410_slider').on('input', function() {
updateFrame(this.value);
});
updateFrame("0");
});
adjustSquares();
})();
</script>