gromacs.geometry ​
Implementation level ​
| Type | Status |
|---|---|
| CML extraction template |  |
| HTML5 representation | |
Template attributes ​
| Attribute | Value |
|---|---|
| source | GROMACS geometry |
| id | gromacs.geometry |
| name | GROMACS geometry |
| xml:base | topTemplate.xml |
Input ​
(linq)8- (4) with 8 cs countercations in TIP4P water
76416
1LIN Nb1 1 5.810 1.559 0.766 -0.4173 -0.1889 -0.2270
1LIN Nb2 2 6.001 1.401 1.000 -0.1596 0.0263 0.1401
1LIN Nb3 3 6.142 1.515 0.709 0.0276 -0.0019 0.1114
1LIN O4 4 5.652 1.515 0.673 0.0837 -0.4086 0.1651
1LIN O5 5 5.852 1.744 0.694 -0.0227 0.3679 -0.2743
1LIN O6 6 5.952 1.487 0.642 -0.3804 0.3800 -0.0091
1LIN O7 7 5.836 1.394 0.880 0.0079 0.0958 -0.0982
1LIN O8 8 5.737 1.652 0.931 -0.3629 -0.1323 0.4503
...
13LIN O23 323 7.240 2.823 8.981 0.0793 0.2503 0.0713
13LIN O24 324 6.996 2.949 8.851 -0.4883 -0.2968 -0.2966
13LIN O25 325 7.453 2.664 9.127 -0.3083 -0.0452 0.1713
14LIN Nb1 326 3.289 8.154 2.339 -0.2450 0.0507 0.1135
14LIN Nb2 327 3.369 7.871 2.167 -0.1957 -0.4587 -0.3182
14LIN Nb3 328 3.226 8.133 2.005 0.2793 -0.0006 0.3156
14LIN O4 329 3.187 8.192 2.491 0.1731 0.3194 -0.5547
14LIN O5 330 3.355 8.339 2.284 0.3083 0.2091 0.0920
14LIN O6 331 3.151 8.169 2.190 -0.1815 -0.2403 -0.3674
14LIN O7 332 3.270 7.952 2.325 -0.1051 0.2506 -0.0708
14LIN O8 333 3.473 8.123 2.418 -0.1356 0.1564 -0.4033
14LIN O9 334 3.539 7.889 2.278 -0.1198 -0.2305 -0.7941
14LIN O10 335 3.217 7.937 2.050 0.0482 0.1952 -0.4407
14LIN O11 336 3.073 8.155 1.897 0.2775 -0.5550 -0.1975
14LIN O12 337 3.328 7.689 2.183 0.2232 0.3580 0.1231
14LIN O13 338 3.421 8.106 2.144 0.1981 -0.1754 -0.0729
14LIN Nb14 339 3.552 8.057 1.948 0.0719 0.2019 0.2251
14LIN Nb15 340 3.471 8.340 2.120 0.1304 0.8115 -0.0654
14LIN Nb16 341 3.615 8.077 2.282 -0.2606 0.1695 -0.2879
14LIN O17 342 3.655 8.020 1.796 -0.0045 0.7444 -0.0477
14LIN O18 343 3.487 7.873 2.002 -0.4919 0.6149 -0.0539
14LIN O19 344 3.689 8.042 2.096 0.2322 -0.2543 0.2241
14LIN O20 345 3.569 8.259 1.962 -0.1200 0.1767 0.0478
14LIN O21 346 3.369 8.087 1.868 -0.3143 -0.6122 -0.2053
14LIN O22 347 3.302 8.321 2.008 0.2259 -0.0363 -0.9310
14LIN O23 348 3.624 8.274 2.236 0.2470 0.1264 -0.4846
14LIN O24 349 3.767 8.054 2.390 -0.2076 0.0012 0.3719
14LIN O25 350 3.512 8.522 2.102 0.4975 0.1911 -0.4630
15LIN Nb1 351 3.302 0.159 7.639 -0.2567 -0.0039 -0.2265
15LIN Nb2 352 3.479 -0.100 7.774 -0.0036 0.1287 0.0719
15LIN Nb3 353 3.644 0.159 7.625 0.0610 0.0055 -0.5074
15LIN O4 354 3.164 0.175 7.515 -0.1929 -0.0504 0.0990
15LIN O5 355 3.336 0.352 7.694 -0.1958 0.0067 -0.1016
15LIN O6 356 3.468 0.173 7.524 0.0677 0.4368 0.2958
15LIN O7 357 3.332 -0.041 7.646 0.1162 0.0356 0.2426
15LIN O8 358 3.200 0.141 7.814 0.1425 -0.3647 0.5087
15LIN O9 359 3.345 -0.076 7.924 0.0724 -0.0856 -0.3348
15LIN O10 360 3.612 -0.041 7.632 -0.2378 -0.1033 0.1232
15LIN O11 361 3.770 0.176 7.488 0.0088 -0.1655 -0.0183
15LIN O12 362 3.481 -0.287 7.750 0.0201 -0.2232 -0.6744
15LIN O13 363 3.480 0.138 7.803 -0.1119 1.0401 -0.7270
15LIN Nb14 364 3.658 0.118 7.965 -0.0047 0.0760 0.2737
15LIN Nb15 365 3.482 0.378 7.831 0.0454 -0.1872 -0.0891
15LIN Nb16 366 3.317 0.118 7.979 -0.2417 -0.0509 0.3626
15LIN O17 367 3.796 0.102 8.089 0.2929 -0.3148 -0.0852
15LIN O18 368 3.626 -0.075 7.911 0.5008 0.0726 -0.2483
15LIN O19 369 3.492 0.105 8.080 0.3718 0.0006 -0.6164
15LIN O20 370 3.629 0.319 7.958 0.6529 -0.8261 0.1062
15LIN O21 371 3.760 0.137 7.789 -0.1041 -0.3168 0.1156
15LIN O22 372 3.617 0.352 7.681 -0.0444 -0.2786 -0.1576
15LIN O23 373 3.349 0.318 7.972 -0.4419 -0.5167 0.1399
15LIN O24 374 3.190 0.103 8.114 0.3737 0.4523 -0.2780
15LIN O25 375 3.481 0.563 7.855 -0.1468 0.1357 -0.5003
16LIN Nb1 376 3.396 0.004 8.713 -0.0350 0.1341 -0.0040
16LIN Nb2 377 3.432 -0.174 8.424 0.3118 -0.2600 0.1679
16LIN Nb3 378 3.696 -0.002 8.554 0.0464 -0.0100 0.0316
16LIN O4 379 3.279 0.138 8.772 -0.5488 -0.5844 -0.1073
16LIN O5 380 3.515 -0.025 8.875 0.6137 -0.0106 -0.4899
16LIN O6 381 3.546 0.112 8.631 0.1285 0.0542 0.3675
16LIN O7 382 3.328 -0.032 8.525 0.1674 -0.2400 -0.4289
16LIN O8 383 3.299 -0.167 8.771 0.0418 -0.8386 0.0243
16LIN O9 384 3.326 -0.311 8.531 0.3518 -0.3545 0.4619
16LIN O10 385 3.574 -0.031 8.394 0.2575 -0.1312 -0.1127
16LIN O11 386 3.814 0.129 8.488 0.4396 0.0944 0.0854
16LIN O12 387 3.348 -0.175 8.257 0.2252 0.0790 -0.3525
16LIN O13 388 3.545 -0.168 8.636 -0.0284 -0.3347 -0.9498
16LIN Nb14 389 3.695 -0.341 8.559 -0.0036 -0.0112 0.3126
16LIN Nb15 390 3.659 -0.164 8.849 0.1232 0.0756 0.0980
16LIN Nb16 391 3.396 -0.337 8.719 -0.2144 -0.1114 -0.3361
16LIN O17 392 3.812 -0.476 8.501 0.3224 0.2539 -0.8260
16LIN O18 393 3.576 -0.314 8.398 0.4334 -0.4553 0.2197
16LIN O19 394 3.544 -0.449 8.642 -0.3953 -0.0560 -0.4263
16LIN O20 395 3.764 -0.307 8.747 0.0286 -0.0176 -0.0911
16LIN O21 396 3.793 -0.172 8.504 0.6435 -0.0798 0.0600
16LIN O22 397 3.764 -0.027 8.744 -0.1101 -0.1476 0.8846
16LIN O23 398 3.517 -0.306 8.879 -0.3891 0.2946 0.2700
16LIN O24 399 3.277 -0.469 8.784 -0.1380 0.2966 0.0280
16LIN O25 400 3.745 -0.163 9.016 0.3388 0.2301 -0.5145
17LIN Nb1 401 7.126 7.474 5.488 -0.1703 0.5631 -0.0439
17LIN Nb2 402 7.009 7.168 5.581 -0.4514 0.0717 0.3383
17LIN Nb3 403 7.166 7.206 5.281 -0.2621 -0.1200 -0.4209
17LIN O4 404 7.050 7.645 5.472 0.1796 0.3863 0.0168
17LIN O5 405 7.319 7.507 5.435 0.4968 -0.4463 0.3467
17LIN O6 406 7.096 7.397 5.305 -0.3835 0.2653 -0.0010
17LIN O7 407 6.968 7.365 5.552 0.0050 0.2319 -0.3449
17LIN O8 408 7.189 7.476 5.681 -1.0270 -0.4676 0.5584
17LIN O9 409 7.091 7.222 5.758 -0.1901 -0.7498 -0.0846
17LIN O10 410 7.000 7.146 5.380 0.3945 -0.2036 -0.5299
17LIN O11 411 7.122 7.170 5.103 -0.4357 -0.0622 0.5615
17LIN O12 412 6.844 7.099 5.634 0.0691 -0.4468 0.3484
17LIN O13 413 7.224 7.255 5.512 -0.1283 0.6296 0.4848
17LIN Nb14 414 7.319 7.035 5.532 0.0340 -0.8202 0.0490
17LIN Nb15 415 7.435 7.341 5.442 0.2719 0.1714 -0.1368
17LIN Nb16 416 7.279 7.302 5.741 -0.0723 0.3550 0.6518
17LIN O17 417 7.394 6.864 5.549 0.2464 0.4839 -0.0619
17LIN O18 418 7.126 7.002 5.587 0.9970 -0.1735 0.1629
17LIN O19 419 7.348 7.112 5.718 0.0590 -0.6416 -0.1315
17LIN O20 420 7.477 7.144 5.470 -0.0488 -0.1097 0.0438
17LIN O21 421 7.254 7.036 5.339 -0.1488 0.3910 -0.3678
17LIN O22 422 7.352 7.286 5.264 -0.0631 0.0801 0.0686
17LIN O23 423 7.445 7.364 5.643 0.3063 -0.5079 -0.1999
17LIN O24 424 7.322 7.340 5.919 0.2702 -0.3976 -0.1347
17LIN O25 425 7.602 7.411 5.388 0.2649 0.3952 0.6043
18LIN Nb1 426 8.280 1.035 6.301 0.2935 -0.0751 0.1194
18LIN Nb2 427 8.124 1.232 6.071 -0.4082 0.0134 -0.3042
18LIN Nb3 428 8.386 1.032 5.977 -0.3928 0.0443 -0.0626
18LIN O4 429 8.361 1.066 6.467 -0.0647 -0.7752 -0.2106
18LIN O5 430 8.303 0.835 6.279 -0.0471 -0.0994 0.2365
18LIN O6 431 8.435 1.058 6.173 0.0155 0.0574 -0.2587
18LIN O7 432 8.219 1.221 6.250 0.0687 0.1727 -0.2709
18LIN O8 433 8.088 0.995 6.355 0.1300 -0.2533 0.1631
18LIN O9 434 7.959 1.159 6.165 -0.1798 -0.2465 0.1226
18LIN O10 435 8.307 1.219 5.984 0.3352 -0.1305 0.1899
18LIN O11 436 8.550 1.061 5.892 0.0435 0.0783 0.5339
18LIN O12 437 8.087 1.414 6.055 -0.4038 -0.0960 -0.0181
18LIN O13 438 8.175 0.995 6.088 0.1005 0.1404 0.3277
18LIN Nb14 439 8.070 0.956 5.875 0.2825 -0.1104 0.1497
18LIN Nb15 440 8.226 0.761 6.107 0.2420 0.0120 0.0620
18LIN Nb16 441 7.963 0.960 6.199 0.3214 0.3744 -0.1981
18LIN O17 442 7.986 0.929 5.710 0.2390 -0.2862 0.4092
18LIN O18 443 8.047 1.158 5.898 -0.6541 0.0927 0.0306
18LIN O19 444 7.915 0.932 6.005 0.5038 -0.2316 -0.0724
18LIN O20 445 8.131 0.770 5.927 0.0928 0.0441 -0.1408
18LIN O21 446 8.261 0.996 5.821 -0.1647 -0.4082 -0.6461
18LIN O22 447 8.390 0.832 6.011 -0.1107 0.1478 0.6837
18LIN O23 448 8.042 0.773 6.193 0.5839 -0.3125 -0.0597
18LIN O24 449 7.800 0.930 6.285 0.0018 -0.2046 -0.8915
18LIN O25 450 8.263 0.578 6.123 0.4088 -0.7076 0.1916
...
216LI LI 792 8.862 5.404 5.017 -0.3867 -0.2730 -0.2475
217SOL OW 793 0.835 4.196 3.614 0.1090 0.5383 0.5716
217SOL HW1 794 0.900 4.164 3.677 -1.1518 -0.5566 1.3404
217SOL HW2 795 0.830 4.127 3.548 0.9829 1.4123 -0.4065
218SOL OW 796 6.757 5.636 6.253 0.0632 -0.7756 0.5798
218SOL HW1 797 6.765 5.606 6.162 -1.1106 -0.2344 0.3025
218SOL HW2 798 6.722 5.560 6.300 -1.0732 -0.4685 0.2352
219SOL OW 799 2.001 0.348 7.652 0.1292 -0.1861 -0.2615
219SOL HW1 800 2.008 0.373 7.559 1.9654 -0.9872 -0.3396
...
9.16090 9.16090 9.16090
Output text ​
xml
<comment class="example.output" id="gromacs.geometry">
<module id="gromacs.geometry">
<molecule id="coordinates">
<atomArray>
<atom elementType="Nb" id="a1" x3="58.1000" y3="15.5900" z3="7.6600" />
<atom elementType="Nb" id="a2" x3="60.0100" y3="14.0100" z3="10.0000" />
<atom elementType="Nb" id="a3" x3="61.4200" y3="15.1500" z3="7.0900" />
<atom elementType="O" id="a4" x3="56.5200" y3="15.1500" z3="6.7300" />
<atom elementType="O" id="a5" x3="58.5200" y3="17.4400" z3="6.9400" />
<atom elementType="O" id="a6" x3="59.5200" y3="14.8700" z3="6.4200" />
<atom elementType="O" id="a7" x3="58.3600" y3="13.9400" z3="8.8000" />
<atom elementType="O" id="a8" x3="57.3700" y3="16.5200" z3="9.3100" />
<atom elementType="O" id="a9" x3="58.9500" y3="15.2100" z3="11.2400" />
<atom elementType="O" id="a10" x3="61.1000" y3="13.5700" z3="8.3200" />
<atom elementType="O" id="a11" x3="62.4300" y3="14.3600" z3="5.7200" />
<atom elementType="O" id="a12" x3="59.9600" y3="12.3500" z3="10.8500" />
<atom elementType="O" id="a13" x3="60.1100" y3="16.1300" z3="8.8500" />
<atom elementType="Nb" id="a14" x3="62.1200" y3="16.6800" z3="10.0300" />
<atom elementType="Nb" id="a15" x3="60.2100" y3="18.2700" z3="7.7100" />
<atom elementType="Nb" id="a16" x3="58.8000" y3="17.1300" z3="10.6100" />
<atom elementType="O" id="a17" x3="63.7000" y3="17.1000" z3="10.9700" />
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<atom elementType="O" id="a20" x3="61.8600" y3="18.3300" z3="8.8800" />
<atom elementType="O" id="a21" x3="62.8500" y3="15.7500" z3="8.4000" />
<atom elementType="O" id="a22" x3="61.2700" y3="17.0600" z3="6.4600" />
<atom elementType="O" id="a23" x3="59.1300" y3="18.7100" z3="9.3700" />
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<atom elementType="Nb" id="a76" x3="63.7800" y3="12.2100" z3="55.5300" />
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<atom elementType="O" id="a79" x3="63.2000" y3="13.9300" z3="55.9800" />
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<atom elementType="O" id="a81" x3="62.0800" y3="11.1400" z3="55.6900" />
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<atom elementType="Li" id="a723" x3="33.9600" y3="89.8500" z3="80.7800" />
<atom elementType="Li" id="a724" x3="64.2500" y3="14.1200" z3="5.1600" />
<atom elementType="Li" id="a725" x3="68.6100" y3="76.8600" z3="54.6300" />
<atom elementType="Li" id="a726" x3="35.0500" y3="81.5100" z3="26.0800" />
<atom elementType="Li" id="a727" x3="71.8400" y3="28.8900" z3="85.5700" />
<atom elementType="Li" id="a728" x3="81.0700" y3="15.4700" z3="61.9300" />
<atom elementType="Li" id="a729" x3="83.0000" y3="7.1400" z3="64.2600" />
<atom elementType="Li" id="a730" x3="33.5200" y3="4.3600" z3="81.1700" />
<atom elementType="Li" id="a731" x3="32.5000" y3="87.0500" z3="84.4000" />
<atom elementType="Li" id="a732" x3="72.5000" y3="84.9400" z3="53.6900" />
<atom elementType="Li" id="a733" x3="59.0600" y3="20.4300" z3="10.0600" />
<atom elementType="Li" id="a734" x3="79.1300" y3="6.3600" z3="61.8500" />
<atom elementType="Li" id="a735" x3="65.9400" y3="14.1600" z3="54.1700" />
<atom elementType="Li" id="a736" x3="76.2600" y3="13.3900" z3="53.3800" />
<atom elementType="Li" id="a737" x3="63.2400" y3="14.0200" z3="9.4700" />
<atom elementType="Li" id="a738" x3="73.3700" y3="67.4200" z3="56.8700" />
<atom elementType="Li" id="a739" x3="37.4300" y3="89.5500" z3="79.8900" />
<atom elementType="Li" id="a740" x3="75.9300" y3="16.2300" z3="64.2500" />
<atom elementType="Li" id="a741" x3="60.4000" y3="29.5200" z3="57.2000" />
<atom elementType="Li" id="a742" x3="30.0300" y3="82.7500" z3="22.2600" />
<atom elementType="Li" id="a743" x3="1.8600" y3="43.4600" z3="56.4000" />
<atom elementType="Li" id="a744" x3="57.4500" y3="14.5400" z3="12.3600" />
<atom elementType="Li" id="a745" x3="74.9900" y3="25.9700" z3="87.7900" />
<atom elementType="Li" id="a746" x3="73.2700" y3="33.9200" z3="2.2900" />
<atom elementType="Li" id="a747" x3="35.8500" y3="75.2400" z3="17.3400" />
<atom elementType="Li" id="a748" x3="59.7800" y3="89.0600" z3="89.9700" />
<atom elementType="Li" id="a749" x3="54.4700" y3="88.9600" z3="84.6600" />
<atom elementType="Li" id="a750" x3="33.0300" y3="67.1000" z3="15.3700" />
<atom elementType="Li" id="a751" x3="86.6700" y3="50.2900" z3="47.7900" />
<atom elementType="Li" id="a752" x3="38.7000" y3="79.7500" z3="20.8200" />
<atom elementType="Li" id="a753" x3="34.5700" y3="0.4100" z3="90.4000" />
<atom elementType="Li" id="a754" x3="62.2400" y3="9.0500" z3="58.6700" />
<atom elementType="Li" id="a755" x3="78.2000" y3="6.7400" z3="50.8400" />
<atom elementType="Li" id="a756" x3="78.0700" y3="29.2500" z3="87.0400" />
<atom elementType="Li" id="a757" x3="62.4000" y3="88.0600" z3="66.7000" />
<atom elementType="Li" id="a758" x3="68.4100" y3="79.6700" z3="52.6000" />
<atom elementType="Li" id="a759" x3="59.7200" y3="33.3500" z3="62.5600" />
<atom elementType="Li" id="a760" x3="2.9000" y3="50.7200" z3="40.4700" />
<atom elementType="Li" id="a761" x3="56.2900" y3="31.4700" z3="59.1800" />
<atom elementType="Li" id="a762" x3="79.8100" y3="88.3800" z3="8.3200" />
<atom elementType="Li" id="a763" x3="37.6400" y3="4.4200" z3="79.9100" />
<atom elementType="Li" id="a764" x3="74.6500" y3="15.2100" z3="60.7100" />
<atom elementType="Li" id="a765" x3="79.5800" y3="14.5500" z3="59.2100" />
<atom elementType="Li" id="a766" x3="81.3400" y3="6.4000" z3="57.9200" />
<atom elementType="Li" id="a767" x3="9.1000" y3="44.4400" z3="43.3800" />
<atom elementType="Li" id="a768" x3="5.4700" y3="48.9300" z3="45.5300" />
<atom elementType="Li" id="a769" x3="87.3200" y3="53.3100" z3="44.8600" />
<atom elementType="Li" id="a770" x3="67.1300" y3="82.6100" z3="61.2200" />
<atom elementType="Li" id="a771" x3="71.0000" y3="75.8100" z3="58.1800" />
<atom elementType="Li" id="a772" x3="54.3100" y3="12.2500" z3="65.9100" />
<atom elementType="Li" id="a773" x3="32.6100" y3="2.9900" z3="86.7300" />
<atom elementType="Li" id="a774" x3="67.2900" y3="84.1600" z3="52.4700" />
<atom elementType="Li" id="a775" x3="91.3800" y3="38.8200" z3="53.3200" />
<atom elementType="Li" id="a776" x3="19.6800" y3="77.2900" z3="22.4100" />
<atom elementType="Li" id="a777" x3="63.5800" y3="9.4400" z3="63.0200" />
<atom elementType="Li" id="a778" x3="63.8100" y3="11.4700" z3="66.5400" />
<atom elementType="Li" id="a779" x3="66.9000" y3="9.9600" z3="60.0000" />
<atom elementType="Li" id="a780" x3="60.3600" y3="39.1700" z3="55.2800" />
<atom elementType="Li" id="a781" x3="5.9900" y3="41.4600" z3="51.0500" />
<atom elementType="Li" id="a782" x3="75.5500" y3="74.9800" z3="57.1900" />
<atom elementType="Li" id="a783" x3="57.8000" y3="15.7000" z3="61.6700" />
<atom elementType="Li" id="a784" x3="76.8100" y3="34.0800" z3="88.5200" />
<atom elementType="Li" id="a785" x3="64.1200" y3="11.9500" z3="49.4500" />
<atom elementType="Li" id="a786" x3="57.1900" y3="89.3100" z3="2.0300" />
<atom elementType="Li" id="a787" x3="53.2000" y3="19.7700" z3="67.4800" />
<atom elementType="Li" id="a788" x3="60.5700" y3="10.4600" z3="52.4300" />
<atom elementType="Li" id="a789" x3="62.5000" y3="15.0000" z3="57.4300" />
<atom elementType="Li" id="a790" x3="72.6000" y3="19.5400" z3="58.6000" />
<atom elementType="Li" id="a791" x3="70.3100" y3="71.4200" z3="59.2100" />
<atom elementType="Li" id="a792" x3="88.6200" y3="54.0400" z3="50.1700" />
</atomArray>
<bondArray />
<formula concise="Li192Nb144O456">
<atomArray count="192 144 456" elementType="Li Nb O" />
</formula>
<property dictRef="cml:molmass">
<scalar units="unit:dalton">22006.91711999997</scalar>
</property>
<propertyList>
<property dictRef="gm:residueNumber">
<array dataType="xsd:integer" size="792">1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9
9 9 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 14 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 16 16
16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22 22 22 22 22
22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 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</array>
</property>
<property dictRef="gm:residueName">
<array dataType="xsd:integer" size="792">LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN
LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN
LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN
LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN
LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN
LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LIN LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI
LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI</array>
</property>
<property dictRef="gm:atomName">
<array dataType="xsd:string" size="792">Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13
Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9
O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4
O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25
Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21 O22 O23 O24 O25 Nb1 Nb2 Nb3 O4 O5 O6 O7 O8 O9 O10 O11 O12 O13 Nb14 Nb15 Nb16 O17 O18 O19 O20 O21
O22 O23 O24 O25 LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI
LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI LI</array>
</property>
</propertyList>
</molecule>
</module>
</comment>Template definition ​
xml
<templateList id="geometry"> <template name="geometry lines" pattern=".*" endPattern="~"> <record repeat="2" /> <templateList> <template name="atoms" id="solvent" pattern="\s*[0-9]+(DMS|SOL|LIG|ELC)\s+.*" endPattern="\s*[0-9]+((?!SOL|LIG|ELC).)+" endPattern2="\s*[0-9]+\.[0-9]+.*" endPattern3="~" repeat="*" endOffset="0"> <record id="atoms" repeat="*">{A5,gm:residueNumber}{A5,gm:residueName}{A5,gm:atomName}{I5,cc:serial}{F8.3,cc:x3}{F8.3,cc:y3}{F8.3,cc:z3}.*</record>
</template> <template name="atoms" id="molecule" pattern="\s*[0-9]+((?!DMS|SOL|LIG|ELC).)+[A-Za-z]+.*" endPattern="\s*[0-9]+(SOL|LIG|ELC)\s+.*" endPattern2="\s*[0-9]+\.[0-9]+.*" endPattern3="~" repeat="*" endOffset="0"> <record id="atoms" repeat="*">{A5,gm:residueNumber}{A5,gm:residueName}{A5,gm:atomName}{I5,cc:serial}{F8.3,cc:x3}{F8.3,cc:y3}{F8.3,cc:z3}.*</record>
</template> <template id="lattice" pattern="\s*[0-9]+\.[0-9]+\s*[0-9]+\.[0-9]+\s*[0-9]+\.[0-9]+.*" endPattern=".*" endPattern2="~" endOffset="0" repeat="*"> <record id="vectors">{1_9F,x:lattice}</record> <transform process="split" xpath=".//cml:array[@dictRef='x:lattice']" dictRef="x:lattice" /> <transform process="operateScalar" xpath=".//cml:scalar" args="operator=multiply operand=10" /> <transform process="pullup" xpath=".//cml:scalar" repeat="2" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:scalar" dictRef="x:lattice" value="0.00000" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="lattice1" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 1]" to="//cml:list[@dictRef='lattice1']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 4]" to="//cml:list[@dictRef='lattice1']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 5]" to="//cml:list[@dictRef='lattice1']" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="lattice2" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 6]" to="//cml:list[@dictRef='lattice2']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 2]" to="//cml:list[@dictRef='lattice2']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 7]" to="//cml:list[@dictRef='lattice2']" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="lattice3" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 8]" to="//cml:list[@dictRef='lattice3']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 9]" to="//cml:list[@dictRef='lattice3']" /> <transform process="copy" xpath="./cml:scalar[@dictRef='x:lattice' and position() = 3]" to="//cml:list[@dictRef='lattice3']" /> <transform process="createArray" xpath="." from="./cml:list[@dictRef='lattice1']/cml:scalar" dataType="xsd:double" dictRef="cc:lattice" /> <transform process="createArray" xpath="." from="./cml:list[@dictRef='lattice2']/cml:scalar" dataType="xsd:double" dictRef="cc:lattice" /> <transform process="createArray" xpath="." from="./cml:list[@dictRef='lattice3']/cml:scalar" dataType="xsd:double" dictRef="cc:lattice" /> <transform process="pullup" xpath=".//cml:array" /> <transform process="delete" xpath=".//cml:scalar" /> <transform process="delete" xpath=".//cml:list" />
</template>
</templateList> <transform process="delete" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='molecule']/preceding-sibling::cml:module[@cmlx:templateRef='solvent']" /> <transform process="delete" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='molecule']/following-sibling::cml:module[@cmlx:templateRef='solvent']" /> <transform process="setValue" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='solvent']//cml:scalar[@dictRef='gm:atomName' and (text() = 'HW1' or text() = 'HW2')]" value="H" /> <transform process="setValue" xpath="/cml:module/cml:module/cml:module[@cmlx:templateRef='solvent']//cml:scalar[@dictRef='gm:atomName' and text() = 'OW']" value="O" /> <transform process="addChild" xpath="/cml:module/cml:module/cml:module/cml:list[@cmlx:templateRef='atoms']/cml:list" elementName="cml:scalar" dictRef="cc:elementType" /> <transform process="addAttribute" xpath="//cml:scalar[@dictRef='cc:elementType']" name="dataType" value="xsd:string" /> <transform process="setValue" xpath="//cml:scalar[@dictRef='cc:elementType']" value="$string(replace(preceding-sibling::cml:scalar[@dictRef='gm:atomName'], '[0-9]',''))" /> <transform process="setValue" xpath="//cml:scalar[@dictRef='cc:elementType']" value="$string(concat(upper-case(substring(./text(), 1, 1)), lower-case(substring(./text(), 2))))" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:x3']" args="operator=multiply operand=10" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:y3']" args="operator=multiply operand=10" /> <transform process="operateScalar" xpath=".//cml:scalar[@dictRef='cc:z3']" args="operator=multiply operand=10" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='cc:x3']" value="$number(round-half-to-even(./text(), 2))" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='cc:y3']" value="$number(round-half-to-even(./text(), 2))" /> <transform process="setValue" xpath=".//cml:scalar[@dictRef='cc:z3']" value="$number(round-half-to-even(./text(), 2))" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:serial']" dataType="xsd:integer" dictRef="cc:serial" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:elementType']" dataType="xsd:string" dictRef="cc:elementType" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:x3']" dataType="xsd:double" dictRef="cc:x3" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:y3']" dataType="xsd:double" dictRef="cc:y3" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='cc:z3']" dataType="xsd:double" dictRef="cc:z3" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='gm:residueNumber']" dataType="xsd:integer" dictRef="gm:residueNumber" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='gm:residueName']" dataType="xsd:integer" dictRef="gm:residueName" /> <transform process="createArray" xpath="." from="//cml:scalar[@dictRef='gm:atomName']" dataType="xsd:string" dictRef="gm:atomName" /> <transform process="pullup" xpath="//cml:list[@cmlx:templateRef='atoms']/cml:list/cml:array" /> <transform process="delete" xpath="//cml:list[count(*)=0]" /> <transform process="addChild" xpath="." elementName="cml:list" dictRef="cc:properties" /> <transform process="move" xpath="//cml:array[@dictRef='gm:residueNumber']" to="//cml:list[@dictRef='cc:properties']" /> <transform process="move" xpath="//cml:array[@dictRef='gm:residueName']" to="//cml:list[@dictRef='cc:properties']" /> <transform process="move" xpath="//cml:array[@dictRef='gm:atomName']" to="//cml:list[@dictRef='cc:properties']" /> <transform process="pullup" xpath="//cml:list[@dictRef='cc:properties']" repeat="2" />
</template>
</templateList>
<transform process="createMolecule" xpath="//cml:module[@cmlx:templateRef='solvent']/cml:list[@cmlx:templateRef='atoms']/cml:array" from="." id="solvent" connect="no" />
<transform process="createMolecule" xpath="//cml:module[@cmlx:templateRef='molecule']/cml:list[@cmlx:templateRef='atoms']/cml:array" from="." id="molecule" connect="no" />
<transform process="createCrystal" xpath="//cml:molecule[@id='solvent']/cml:atomArray" lattice=".//cml:module[@cmlx:templateRef='lattice']" id="coordinates" connect="no" />
<transform process="createCrystal" xpath="//cml:molecule[@id='molecule']/cml:atomArray" lattice=".//cml:module[@cmlx:templateRef='lattice']" id="coordinates" connect="no" />
<transform process="delete" xpath="//cml:module[@cmlx:templateRef='solvent']/preceding::cml:list[@dictRef='cc:properties']" />
<transform process="delete" xpath="//cml:scalar[@dictRef='cc:serial']" />
<transform process="delete" xpath="//cml:scalar[@dictRef='cc:atomicNumber']" />
<transform process="addChild" xpath="//cml:molecule" elementName="cml:propertyList" />
<transform process="move" xpath="//cml:list[@dictRef='cc:properties']/cml:array" to="//cml:molecule/cml:propertyList" />
<transform process="createWrapperProperty" xpath="//cml:molecule/cml:propertyList/*" />
<transform process="createWrapper" xpath="//cml:molecule/cml:propertyList/cml:module" elementName="cml:property" />
<transform process="move" xpath="//cml:molecule[@id='coordinates']" to="/cml:module" />
<transform process="delete" xpath="//cml:module" />
<transform process="delete" xpath="//cml:list" />