I've run some calculations with the xtb
software. From its output I got XYZ
and MOL
files with the system's structure information, and also a charge
file with the calculated charges.
I would like to merge these two files into one or to create a new one (one that supports the charges like MOL
or MOL2
) with the charges added.
As there are a lot of files to merge, making the process automatic will decrease the errors.
Here is the MOL
output:
xtb: 6.5.1 (579679a)
08092221593D
140170 0 0 0 999 V2000
2.6154 6.4064 0.9956 C 0 0 0 0 0 0 0 0 0 0 0 0
4.8578 2.7738 1.5382 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7755 1.6888 2.8422 C 0 0 0 0 0 0 0 0 0 0 0 0
12.3803 4.0139 3.6724 C 0 0 0 0 0 0 0 0 0 0 0 0
14.4811 8.0604 3.5495 C 0 0 0 0 0 0 0 0 0 0 0 0
14.7628 12.5956 3.8804 C 0 0 0 0 0 0 0 0 0 0 0 0
12.2314 15.9121 5.2439 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0491 16.1020 6.2971 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3849 13.8269 6.4268 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9317 10.3116 6.0240 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5655 5.6280 2.1771 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1268 2.3726 2.8718 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0773 2.2650 4.1013 C 0 0 0 0 0 0 0 0 0 0 0 0
12.0035 5.2635 4.2054 C 0 0 0 0 0 0 0 0 0 0 0 0
13.5944 9.1063 3.2349 C 0 0 0 0 0 0 0 0 0 0 0 0
13.8120 13.3380 3.1439 C 0 0 0 0 0 0 0 0 0 0 0 0
11.1970 16.3391 4.3698 C 0 0 0 0 0 0 0 0 0 0 0 0
7.1033 16.0816 5.2396 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7923 13.4377 5.2013 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8727 9.6802 4.7586 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3785 7.7477 1.0115 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9239 3.7276 1.2646 C 0 0 0 0 0 0 0 0 0 0 0 0
7.4778 1.5634 2.4333 C 0 0 0 0 0 0 0 0 0 0 0 0
11.4867 2.9689 3.6452 C 0 0 0 0 0 0 0 0 0 0 0 0
14.0231 6.7778 3.7699 C 0 0 0 0 0 0 0 0 0 0 0 0
14.8634 11.2314 3.7574 C 0 0 0 0 0 0 0 0 0 0 0 0
13.2537 15.1192 4.8081 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3682 16.3578 6.0715 C 0 0 0 0 0 0 0 0 0 0 0 0
5.3899 14.7451 6.4745 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4918 11.5427 6.1782 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0483 6.2519 3.3426 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1735 2.7427 3.8532 C 0 0 0 0 0 0 0 0 0 0 0 0
8.0189 2.3406 5.0369 C 0 0 0 0 0 0 0 0 0 0 0 0
10.7860 5.3145 4.9239 C 0 0 0 0 0 0 0 0 0 0 0 0
12.2136 8.7905 3.1968 C 0 0 0 0 0 0 0 0 0 0 0 0
13.1029 12.6442 2.1282 C 0 0 0 0 0 0 0 0 0 0 0 0
11.4425 16.2051 2.9792 C 0 0 0 0 0 0 0 0 0 0 0 0
7.5166 16.6283 3.9997 C 0 0 0 0 0 0 0 0 0 0 0 0
4.1292 14.1863 4.0465 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2291 10.4449 3.6202 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7997 5.4842 4.5093 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3387 2.3324 5.2019 C 0 0 0 0 0 0 0 0 0 0 0 0
8.1671 3.0483 6.2595 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1209 6.5319 5.2123 C 0 0 0 0 0 0 0 0 0 0 0 0
11.2534 9.6203 2.5774 C 0 0 0 0 0 0 0 0 0 0 0 0
12.3500 13.3264 1.1466 C 0 0 0 0 0 0 0 0 0 0 0 0
10.5758 16.8019 2.0305 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5915 16.7546 2.9314 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5515 13.8555 2.7932 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1840 9.8586 2.3280 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1162 8.4415 2.2180 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1644 4.3427 2.2940 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3936 1.8785 3.2932 C 0 0 0 0 0 0 0 0 0 0 0 0
10.2644 3.0226 4.3495 C 0 0 0 0 0 0 0 0 0 0 0 0
12.6538 6.5197 3.9629 C 0 0 0 0 0 0 0 0 0 0 0 0
13.8757 10.5024 3.0610 C 0 0 0 0 0 0 0 0 0 0 0 0
13.2525 14.6070 3.4858 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8563 16.6076 4.7638 C 0 0 0 0 0 0 0 0 0 0 0 0
5.8565 15.3993 5.3093 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9690 12.2844 5.0728 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8844 7.6630 3.3789 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1807 3.7133 3.5633 C 0 0 0 0 0 0 0 0 0 0 0 0
6.6914 2.0049 4.6747 C 0 0 0 0 0 0 0 0 0 0 0 0
10.0670 4.1338 5.2103 C 0 0 0 0 0 0 0 0 0 0 0 0
11.7676 7.6173 3.8365 C 0 0 0 0 0 0 0 0 0 0 0 0
12.9660 11.2456 2.2735 C 0 0 0 0 0 0 0 0 0 0 0 0
12.3952 15.2449 2.5579 C 0 0 0 0 0 0 0 0 0 0 0 0
8.8910 16.8909 3.7647 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1088 15.2137 4.1167 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6925 11.7802 3.7750 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1823 6.1326 5.6093 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2381 2.5050 6.0837 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2235 2.8209 7.2901 C 0 0 0 0 0 0 0 0 0 0 0 0
9.1335 6.5533 6.2147 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8922 9.4440 2.8898 C 0 0 0 0 0 0 0 0 0 0 0 0
11.4589 12.5836 0.3322 C 0 0 0 0 0 0 0 0 0 0 0 0
10.8812 16.6308 0.6495 C 0 0 0 0 0 0 0 0 0 0 0 0
7.0004 17.5061 1.7965 C 0 0 0 0 0 0 0 0 0 0 0 0
3.7126 14.7775 1.7314 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3234 10.7199 1.2150 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5821 8.2989 4.6110 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3389 4.1816 4.6048 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6556 2.0803 5.6374 C 0 0 0 0 0 0 0 0 0 0 0 0
9.0411 4.1580 6.1804 C 0 0 0 0 0 0 0 0 0 0 0 0
10.4451 7.5992 4.3331 C 0 0 0 0 0 0 0 0 0 0 0 0
11.7517 10.6933 1.7928 C 0 0 0 0 0 0 0 0 0 0 0 0
12.2292 14.7312 1.2441 C 0 0 0 0 0 0 0 0 0 0 0 0
9.3032 17.2384 2.4518 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4037 15.9878 2.9656 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9370 12.5850 2.6348 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1060 7.4876 5.6696 C 0 0 0 0 0 0 0 0 0 0 0 0
2.2582 3.3935 5.7862 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0214 2.2581 7.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
8.7063 5.3904 6.7904 C 0 0 0 0 0 0 0 0 0 0 0 0
9.5223 8.5497 3.8597 C 0 0 0 0 0 0 0 0 0 0 0 0
11.0732 11.3403 0.7420 C 0 0 0 0 0 0 0 0 0 0 0 0
11.6303 15.5656 0.2674 C 0 0 0 0 0 0 0 0 0 0 0 0
8.3155 17.7389 1.5616 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5773 15.8218 1.8258 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6471 12.0340 1.3638 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8822 5.9347 0.0623 H 0 0 0 0 0 0 0 0 0 0 0 0
5.4684 2.3857 0.7370 H 0 0 0 0 0 0 0 0 0 0 0 0
9.5780 1.4859 2.1486 H 0 0 0 0 0 0 0 0 0 0 0 0
13.3259 3.9246 3.1576 H 0 0 0 0 0 0 0 0 0 0 0 0
15.5442 8.2537 3.5477 H 0 0 0 0 0 0 0 0 0 0 0 0
15.4188 13.1152 4.5637 H 0 0 0 0 0 0 0 0 0 0 0 0
12.1781 16.1740 6.2901 H 0 0 0 0 0 0 0 0 0 0 0 0
7.7339 15.8416 7.2958 H 0 0 0 0 0 0 0 0 0 0 0 0
4.0866 13.3367 7.3404 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5927 9.7794 6.8990 H 0 0 0 0 0 0 0 0 0 0 0 0
2.4639 8.3002 0.0888 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8109 4.0686 0.2469 H 0 0 0 0 0 0 0 0 0 0 0 0
7.2725 1.2664 1.4155 H 0 0 0 0 0 0 0 0 0 0 0 0
11.7249 2.0829 3.0746 H 0 0 0 0 0 0 0 0 0 0 0 0
14.7318 5.9701 3.8829 H 0 0 0 0 0 0 0 0 0 0 0 0
15.6161 10.6960 4.3178 H 0 0 0 0 0 0 0 0 0 0 0 0
13.9932 14.7651 5.5108 H 0 0 0 0 0 0 0 0 0 0 0 0
10.0670 16.2875 6.8912 H 0 0 0 0 0 0 0 0 0 0 0 0
5.8578 14.9567 7.4236 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5740 11.9580 7.1708 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8329 5.5465 6.4447 H 0 0 0 0 0 0 0 0 0 0 0 0
3.2195 1.9677 7.0198 H 0 0 0 0 0 0 0 0 0 0 0 0
7.4570 3.1395 8.2953 H 0 0 0 0 0 0 0 0 0 0 0 0
8.7267 7.5030 6.5288 H 0 0 0 0 0 0 0 0 0 0 0 0
9.1601 10.0959 2.4370 H 0 0 0 0 0 0 0 0 0 0 0 0
10.9540 13.0736 -0.4860 H 0 0 0 0 0 0 0 0 0 0 0 0
10.3958 17.2479 -0.0899 H 0 0 0 0 0 0 0 0 0 0 0 0
6.2625 17.8432 1.0853 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1458 14.6441 0.8228 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1745 10.3292 0.2202 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6889 7.9539 6.5489 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4525 3.5570 6.4847 H 0 0 0 0 0 0 0 0 0 0 0 0
5.2888 2.1084 7.7794 H 0 0 0 0 0 0 0 0 0 0 0 0
7.9753 5.4063 7.5844 H 0 0 0 0 0 0 0 0 0 0 0 0
8.5000 8.5068 4.2048 H 0 0 0 0 0 0 0 0 0 0 0 0
10.2424 10.8390 0.2682 H 0 0 0 0 0 0 0 0 0 0 0 0
11.7390 15.3140 -0.7771 H 0 0 0 0 0 0 0 0 0 0 0 0
8.6218 18.2523 0.6630 H 0 0 0 0 0 0 0 0 0 0 0 0
4.6873 16.4912 0.9873 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7536 12.6473 0.4827 H 0 0 0 0 0 0 0 0 0 0 0 0
1 11 4 0 0 0 0
2 12 4 0 0 0 0
3 13 4 0 0 0 0
4 14 4 0 0 0 0
5 15 4 0 0 0 0
6 16 4 0 0 0 0
7 17 4 0 0 0 0
8 18 4 0 0 0 0
9 19 4 0 0 0 0
10 20 4 0 0 0 0
1 21 2 0 0 0 0
2 22 2 0 0 0 0
3 23 2 0 0 0 0
4 24 2 0 0 0 0
5 25 2 0 0 0 0
6 26 2 0 0 0 0
7 27 2 0 0 0 0
8 28 2 0 0 0 0
9 29 2 0 0 0 0
10 30 2 0 0 0 0
11 31 4 0 0 0 0
12 32 4 0 0 0 0
13 33 4 0 0 0 0
14 34 4 0 0 0 0
15 35 4 0 0 0 0
16 36 4 0 0 0 0
17 37 4 0 0 0 0
18 38 4 0 0 0 0
19 39 4 0 0 0 0
20 40 4 0 0 0 0
31 41 4 0 0 0 0
32 42 4 0 0 0 0
33 43 4 0 0 0 0
34 44 4 0 0 0 0
35 45 4 0 0 0 0
36 46 4 0 0 0 0
37 47 4 0 0 0 0
38 48 4 0 0 0 0
39 49 4 0 0 0 0
40 50 4 0 0 0 0
21 51 4 0 0 0 0
50 51 4 0 0 0 0
11 52 4 0 0 0 0
22 52 4 0 0 0 0
12 53 4 0 0 0 0
23 53 4 0 0 0 0
13 54 4 0 0 0 0
24 54 4 0 0 0 0
14 55 1 0 0 0 0
25 55 4 0 0 0 0
15 56 1 0 0 0 0
26 56 4 0 0 0 0
16 57 4 0 0 0 0
27 57 4 0 0 0 0
17 58 4 0 0 0 0
28 58 4 0 0 0 0
18 59 4 0 0 0 0
29 59 4 0 0 0 0
19 60 4 0 0 0 0
30 60 4 0 0 0 0
31 61 4 0 0 0 0
51 61 4 0 0 0 0
32 62 4 0 0 0 0
52 62 4 0 0 0 0
33 63 4 0 0 0 0
53 63 4 0 0 0 0
34 64 4 0 0 0 0
54 64 4 0 0 0 0
35 65 4 0 0 0 0
55 65 4 0 0 0 0
36 66 4 0 0 0 0
56 66 4 0 0 0 0
37 67 4 0 0 0 0
57 67 4 0 0 0 0
38 68 4 0 0 0 0
58 68 4 0 0 0 0
39 69 4 0 0 0 0
59 69 4 0 0 0 0
40 70 4 0 0 0 0
60 70 4 0 0 0 0
41 71 4 0 0 0 0
42 72 4 0 0 0 0
43 73 4 0 0 0 0
44 74 4 0 0 0 0
45 75 4 0 0 0 0
46 76 4 0 0 0 0
47 77 4 0 0 0 0
48 78 4 0 0 0 0
49 79 4 0 0 0 0
50 80 4 0 0 0 0
20 81 4 0 0 0 0
61 81 4 0 0 0 0
41 82 4 0 0 0 0
62 82 4 0 0 0 0
42 83 4 0 0 0 0
63 83 4 0 0 0 0
43 84 4 0 0 0 0
64 84 4 0 0 0 0
44 85 1 0 0 0 0
65 85 4 0 0 0 0
45 86 4 0 0 0 0
66 86 4 0 0 0 0
46 87 4 0 0 0 0
67 87 4 0 0 0 0
47 88 4 0 0 0 0
68 88 4 0 0 0 0
48 89 4 0 0 0 0
69 89 4 0 0 0 0
49 90 4 0 0 0 0
70 90 4 0 0 0 0
71 91 2 0 0 0 0
81 91 4 0 0 0 0
72 92 2 0 0 0 0
82 92 4 0 0 0 0
73 93 2 0 0 0 0
83 93 4 0 0 0 0
74 94 2 0 0 0 0
84 94 4 0 0 0 0
75 95 2 0 0 0 0
85 95 4 0 0 0 0
76 96 2 0 0 0 0
86 96 4 0 0 0 0
77 97 2 0 0 0 0
87 97 4 0 0 0 0
78 98 2 0 0 0 0
88 98 4 0 0 0 0
79 99 2 0 0 0 0
89 99 4 0 0 0 0
80100 2 0 0 0 0
90100 4 0 0 0 0
1101 1 0 0 0 0
2102 1 0 0 0 0
3103 1 0 0 0 0
4104 1 0 0 0 0
5105 1 0 0 0 0
6106 1 0 0 0 0
7107 1 0 0 0 0
8108 1 0 0 0 0
9109 1 0 0 0 0
10110 1 0 0 0 0
21111 1 0 0 0 0
22112 1 0 0 0 0
23113 1 0 0 0 0
24114 1 0 0 0 0
25115 1 0 0 0 0
26116 1 0 0 0 0
27117 1 0 0 0 0
28118 1 0 0 0 0
29119 1 0 0 0 0
30120 1 0 0 0 0
71121 1 0 0 0 0
72122 1 0 0 0 0
73123 1 0 0 0 0
74124 1 0 0 0 0
75125 1 0 0 0 0
76126 1 0 0 0 0
77127 1 0 0 0 0
78128 1 0 0 0 0
79129 1 0 0 0 0
80130 1 0 0 0 0
91131 1 0 0 0 0
92132 1 0 0 0 0
93133 1 0 0 0 0
94134 1 0 0 0 0
95135 1 0 0 0 0
96136 1 0 0 0 0
97137 1 0 0 0 0
98138 1 0 0 0 0
99139 1 0 0 0 0
100140 1 0 0 0 0
M END
Here is the charge
file:
-0.03722231
-0.03646360
-0.03466408
-0.03460579
-0.03700567
-0.03830432
-0.03743637
-0.03678821
-0.03708334
-0.03759946
0.00341706
0.00262820
0.00029768
0.00086030
0.00393716
0.00505315
0.00341478
0.00243039
0.00241051
0.00266387
-0.03697613
-0.03683137
-0.03764684
-0.03827265
-0.03653021
-0.03436292
-0.03497639
-0.03671793
-0.03724731
-0.03728009
0.00104757
0.00049263
0.00207651
0.00321830
0.00222174
0.00127540
0.00206366
0.00229686
0.00224290
0.00189821
0.00330899
0.00455347
0.00472102
0.00365930
0.00259012
0.00170297
0.00134970
0.00213949
0.00282399
0.00313627
0.00237572
0.00250757
0.00375430
0.00511583
0.00341053
0.00041637
0.00067468
0.00294210
0.00339482
0.00307549
0.00225484
0.00229451
0.00190616
0.00130541
0.00249185
0.00319625
0.00168094
0.00045411
0.00125032
0.00200113
-0.03773413
-0.03747374
-0.03777553
-0.03792015
-0.03639454
-0.03541961
-0.03566344
-0.03655314
-0.03719833
-0.03727186
0.00273925
0.00195800
0.00134150
0.00181929
0.00281034
0.00384329
0.00486636
0.00431232
0.00314034
0.00260470
-0.03713453
-0.03636143
-0.03555836
-0.03549570
-0.03669229
-0.03802718
-0.03766679
-0.03750089
-0.03776054
-0.03752020
0.03161620
0.03281056
0.03326035
0.03226115
0.03226474
0.03351993
0.03406948
0.03286813
0.03183449
0.03171993
0.03197441
0.03313788
0.03413108
0.03325210
0.03214467
0.03243500
0.03333614
0.03256787
0.03146893
0.03150533
0.03233615
0.03409028
0.03608529
0.03407825
0.03155533
0.03339691
0.03529538
0.03388412
0.03228017
0.03141505
0.03254266
0.03420700
0.03527684
0.03276537
0.03177783
0.03467319
0.03596630
0.03361589
0.03217072
0.03167577
iodata
could read in the XYZ, and then a simple python one liner could probably fetch the charges, and add them to the iodata object created for the XYZ, and then it is just a click of a button to output a mol2 file $\endgroup$file.charge
to be added as the last column infile.MOL
, and you want to do this for 100s of files? $\endgroup$