Dear friends,
I have a file with thousands of molecule coordinates. Everyone should have a name but unfortunately the names are missing. I have to put a name for everyone to start working. For example MOLECULE1, MOLECULE2, etc.
The file with five molecules is attached.
The names must be at the line just below @<TRIPOS>MOLECULE
Is there an easy way to do this?
Thank you very much.
Clara
You can't do file attachments as a new poster. Please copy and past a few lines of the file into a post, perhaps in output tags (the button in the editor between the x and the []).
Thank you. I didn't know.
@<TRIPOS>MOLECULE
49 52 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 3.2145 3.5607 -4.5647 C3 1 LIG1 -0.0308
2 C 3.7870 4.4501 -3.4593 C3 1 LIG1 0.1352
3 C 3.6398 3.7859 -2.1047 C2 1 LIG1 0.2511
4 O 4.1284 2.7355 -1.7472 O2 1 LIG1 -0.2724
5 N 2.8515 4.6051 -1.3810 Nam 1 LIG1 -0.2196
6 C 2.4900 5.6869 -2.0803 C2 1 LIG1 0.3099
7 O 1.7832 6.5716 -1.6389 O2 1 LIG1 -0.2522
8 N 2.9962 5.6859 -3.3267 Nam 1 LIG1 -0.2813
9 C 2.4456 4.3460 0.0026 C3 1 LIG1 0.0489
10 C 1.1540 3.5697 0.0103 Car 1 LIG1 -0.0288
11 C -0.0555 4.2421 0.0255 Car 1 LIG1 -0.0570
12 C -1.2460 3.5373 0.0330 Car 1 LIG1 -0.0607
13 C -1.2346 2.1577 0.0196 Car 1 LIG1 -0.0478
14 C -0.0180 1.4730 0.0101 Car 1 LIG1 0.0593
15 C 1.1799 2.1908 0.0026 Car 1 LIG1 -0.0431
16 C 0.0021 -0.0041 0.0020 C2 1 LIG1 0.3389
17 O 1.0621 -0.5970 -0.0113 O2 1 LIG1 -0.2450
18 O -1.1553 -0.6934 0.0094 O3 1 LIG1 -0.4645
19 C -1.0596 -2.1423 0.0007 C3 1 LIG1 0.0820
20 C 5.2327 4.7730 -3.7362 Car 1 LIG1 -0.0118
21 C 6.2282 3.9309 -3.2765 Car 1 LIG1 -0.0524
22 C 7.5551 4.2237 -3.5282 Car 1 LIG1 -0.0159
23 C 7.8917 5.3638 -4.2429 Car 1 LIG1 0.1621
24 C 6.8910 6.2095 -4.7063 Car 1 LIG1 0.1624
25 C 5.5609 5.9073 -4.4542 Car 1 LIG1 -0.0106
26 O 7.1988 7.3311 -5.4133 O3 1 LIG1 -0.4849
27 C 8.5508 7.7945 -5.3277 C3 1 LIG1 0.1237
28 C 9.4839 6.5904 -5.5137 C3 1 LIG1 0.1237
29 O 9.2030 5.6415 -4.4790 O3 1 LIG1 -0.4849
30 H 3.2495 4.0938 -5.5148 1 1 LIG1 0.0258
31 H 3.8049 2.6474 -4.6386 1 1 LIG1 0.0258
32 H 2.1811 3.3071 -4.3283 1 1 LIG1 0.0258
33 H 2.8663 6.3665 -4.0056 1 1 LIG1 0.1516
34 H 2.3033 5.2932 0.5229 1 1 LIG1 0.0519
35 H 3.2201 3.7676 0.5062 1 1 LIG1 0.0519
36 H -0.0702 5.3220 0.0311 1 1 LIG1 0.0621
37 H -2.1864 4.0682 0.0446 1 1 LIG1 0.0618
38 H -2.1646 1.6088 0.0206 1 1 LIG1 0.0626
39 H 2.1245 1.6673 -0.0090 1 1 LIG1 0.0629
40 H -0.5315 -2.4661 -0.8961 1 1 LIG1 0.0661
41 H -0.5145 -2.4757 0.8837 1 1 LIG1 0.0661
42 H -2.0611 -2.5725 0.0079 1 1 LIG1 0.0661
43 H 5.9684 3.0426 -2.7200 1 1 LIG1 0.0622
44 H 8.3308 3.5644 -3.1678 1 1 LIG1 0.0655
45 H 4.7812 6.5614 -4.8156 1 1 LIG1 0.0659
46 H 8.7236 8.2460 -4.3508 1 1 LIG1 0.0731
47 H 8.7384 8.5294 -6.1106 1 1 LIG1 0.0731
48 H 10.5219 6.9152 -5.4427 1 1 LIG1 0.0731
49 H 9.3073 6.1348 -6.4881 1 1 LIG1 0.0731
@<TRIPOS>BOND
1 1 2 1
2 1 30 1
3 1 31 1
4 1 32 1
5 2 8 1
6 2 3 1
7 2 20 1
8 3 4 2
9 3 5 am
10 5 6 am
11 5 9 1
12 6 7 2
13 6 8 am
14 8 33 1
15 9 10 1
16 9 34 1
17 9 35 1
18 10 15 ar
19 10 11 ar
20 11 12 ar
21 11 36 1
22 12 13 ar
23 12 37 1
24 13 14 ar
25 13 38 1
26 14 15 ar
27 14 16 1
28 15 39 1
29 16 17 2
30 16 18 1
31 18 19 1
32 19 40 1
33 19 41 1
34 19 42 1
35 20 25 ar
36 20 21 ar
37 21 22 ar
38 21 43 1
39 22 23 ar
40 22 44 1
41 23 29 1
42 23 24 ar
43 24 25 ar
44 24 26 1
45 25 45 1
46 26 27 1
47 27 28 1
48 27 46 1
49 27 47 1
50 28 29 1
51 28 48 1
52 28 49 1
@<TRIPOS>MOLECULE
53 54 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 5.5013 -0.3856 1.7029 C3 1 LIG1 -0.0489
2 C 5.0325 -0.3046 0.2487 C3 1 LIG1 0.0171
3 N 3.6496 -0.7786 0.1542 Nam 1 LIG1 -0.2686
4 C 2.5909 0.1335 0.2264 Car 1 LIG1 0.0364
5 C 1.2897 -0.2907 -0.0094 Car 1 LIG1 -0.0403
6 C 0.2470 0.6122 0.0622 Car 1 LIG1 -0.0600
7 C 0.4976 1.9372 0.3682 Car 1 LIG1 -0.0616
8 C 1.7921 2.3627 0.6034 Car 1 LIG1 -0.0600
9 C 2.8392 1.4649 0.5335 Car 1 LIG1 -0.0403
10 C 3.3970 -2.0932 -0.0021 C2 1 LIG1 0.2604
11 O 2.2571 -2.4775 -0.1576 O2 1 LIG1 -0.2712
12 C 4.5308 -3.0858 0.0162 C3 1 LIG1 0.1763
13 H 5.2437 -2.8088 0.7928 1 1 LIG1 0.0830
14 C 5.2320 -3.0842 -1.3437 C3 1 LIG1 -0.0189
15 O 4.0165 -4.3916 0.2854 O3 1 LIG1 -0.4491
16 C 4.8315 -5.2491 0.9344 C2 1 LIG1 0.3327
17 O 5.9486 -4.8964 1.2623 O2 1 LIG1 -0.2456
18 C 4.3858 -6.5612 1.2340 C2 1 LIG1 0.0231
19 C 5.2018 -7.4198 1.8838 C2 1 LIG1 -0.0477
20 C 4.7399 -8.7799 2.1944 Car 1 LIG1 -0.0211
21 C 3.4549 -9.1879 1.8180 Car 1 LIG1 -0.0509
22 C 3.0245 -10.4632 2.1105 Car 1 LIG1 -0.0157
23 C 3.8624 -11.3468 2.7780 Car 1 LIG1 0.1615
24 C 5.1440 -10.9479 3.1563 Car 1 LIG1 0.1620
25 C 5.5857 -9.6731 2.8625 Car 1 LIG1 -0.0091
26 O 5.9610 -11.8166 3.8102 O3 1 LIG1 -0.4914
27 C 7.2603 -11.3412 4.1676 C3 1 LIG1 0.0790
28 O 3.4327 -12.6033 3.0627 O3 1 LIG1 -0.4915
29 C 2.1095 -12.9464 2.6463 C3 1 LIG1 0.0790
30 H 4.8602 0.2375 2.3265 1 1 LIG1 0.0245
31 H 5.4472 -1.4192 2.0450 1 1 LIG1 0.0245
32 H 6.5302 -0.0330 1.7731 1 1 LIG1 0.0245
33 H 5.6736 -0.9277 -0.3749 1 1 LIG1 0.0466
34 H 5.0865 0.7289 -0.0934 1 1 LIG1 0.0466
35 H 1.0934 -1.3254 -0.2488 1 1 LIG1 0.0636
36 H -0.7651 0.2830 -0.1214 1 1 LIG1 0.0618
37 H -0.3190 2.6422 0.4191 1 1 LIG1 0.0618
38 H 1.9845 3.3983 0.8422 1 1 LIG1 0.0618
39 H 3.8500 1.7978 0.7173 1 1 LIG1 0.0636
40 H 5.7060 -2.1163 -1.5070 1 1 LIG1 0.0270
41 H 5.9896 -3.8676 -1.3628 1 1 LIG1 0.0270
42 H 4.4999 -3.2675 -2.1302 1 1 LIG1 0.0270
43 H 3.3941 -6.8744 0.9429 1 1 LIG1 0.0689
44 H 6.1935 -7.1067 2.1749 1 1 LIG1 0.0626
45 H 2.8012 -8.5031 1.2982 1 1 LIG1 0.0625
46 H 2.0328 -10.7769 1.8196 1 1 LIG1 0.0655
47 H 6.5797 -9.3645 3.1510 1 1 LIG1 0.0661
48 H 7.8074 -12.1312 4.6821 1 1 LIG1 0.0660
49 H 7.8016 -11.0514 3.2670 1 1 LIG1 0.0660
50 H 7.1629 -10.4783 4.8264 1 1 LIG1 0.0660
51 H 1.3935 -12.2769 3.1231 1 1 LIG1 0.0660
52 H 2.0326 -12.8489 1.5634 1 1 LIG1 0.0660
53 H 1.8929 -13.9749 2.9349 1 1 LIG1 0.0660
@<TRIPOS>BOND
1 1 2 1
2 1 30 1
3 1 31 1
4 1 32 1
5 2 3 1
6 2 33 1
7 2 34 1
8 3 4 1
9 3 10 am
10 4 9 ar
11 4 5 ar
12 5 6 ar
13 5 35 1
14 6 7 ar
15 6 36 1
16 7 8 ar
17 7 37 1
18 8 9 ar
19 8 38 1
20 9 39 1
21 10 11 2
22 10 12 1
23 12 13 1
24 12 14 1
25 12 15 1
26 14 40 1
27 14 41 1
28 14 42 1
29 15 16 1
30 16 17 2
31 16 18 1
32 18 19 2
33 18 43 1
34 19 20 1
35 19 44 1
36 20 25 ar
37 20 21 ar
38 21 22 ar
39 21 45 1
40 22 23 ar
41 22 46 1
42 23 24 ar
43 23 28 1
44 24 25 ar
45 24 26 1
46 25 47 1
47 26 27 1
48 27 48 1
49 27 49 1
50 27 50 1
51 28 29 1
52 29 51 1
53 29 52 1
54 29 53 1
@<TRIPOS>MOLECULE
37 38 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C -2.6291 2.3319 3.6320 C3 1 LIG1 -0.0608
2 C -1.9645 3.4514 2.8282 C3 1 LIG1 -0.0242
3 C -0.9863 2.8545 1.8495 Car 1 LIG1 -0.0099
4 C -1.2096 2.4593 0.5687 Car 1 LIG1 -0.0510
5 C -0.1738 1.9302 -0.1605 Car 1 LIG1 -0.0472
6 C 1.0622 1.8436 0.4707 Car 1 LIG1 0.0144
7 S 0.6970 2.5128 2.0837 S2 1 LIG1 -0.0937
8 C 2.2887 1.3522 -0.0340 C2 1 LIG1 -0.0214
9 C 3.3707 2.1771 -0.1176 C2 1 LIG1 0.0999
10 C 4.7348 1.7914 -0.2256 C2 1 LIG1 0.2663
11 O 5.1648 0.6524 -0.2606 O2 1 LIG1 -0.2682
12 N 5.4619 2.9243 -0.2815 Nam 1 LIG1 -0.2512
13 C 4.6439 3.9879 -0.2157 C2 1 LIG1 0.1468
14 S 5.1517 5.6224 -0.2543 S2 1 LIG1 -0.0177
15 N 3.3651 3.5779 -0.1207 Nam 1 LIG1 -0.2671
16 C 2.1835 4.4395 -0.0332 C3 1 LIG1 0.1161
17 C 1.9548 4.8339 1.4032 C2 1 LIG1 0.3248
18 O 2.6935 4.4244 2.2671 O2 1 LIG1 -0.2491
19 O 0.9303 5.6403 1.7228 O3 1 LIG1 -0.4668
20 C 0.7705 5.9786 3.1257 C3 1 LIG1 0.0817
21 C 6.9210 2.9867 -0.3970 C3 1 LIG1 0.0103
22 H -3.1570 1.6617 2.9536 1 1 LIG1 0.0233
23 H -1.8671 1.7729 4.1750 1 1 LIG1 0.0233
24 H -3.3366 2.7637 4.3399 1 1 LIG1 0.0233
25 H -1.4365 4.1216 3.5066 1 1 LIG1 0.0316
26 H -2.7265 4.0105 2.2851 1 1 LIG1 0.0316
27 H -2.1920 2.5565 0.1307 1 1 LIG1 0.0626
28 H -0.3116 1.6005 -1.1797 1 1 LIG1 0.0629
29 H 2.3680 0.3235 -0.3532 1 1 LIG1 0.0649
30 H 2.3411 5.3345 -0.6351 1 1 LIG1 0.0584
31 H 1.3123 3.9003 -0.4051 1 1 LIG1 0.0584
32 H -0.0921 6.6341 3.2455 1 1 LIG1 0.0661
33 H 0.6175 5.0674 3.7040 1 1 LIG1 0.0661
34 H 1.6662 6.4882 3.4809 1 1 LIG1 0.0661
35 H 7.3265 1.9755 -0.4301 1 1 LIG1 0.0433
36 H 7.1909 3.5165 -1.3105 1 1 LIG1 0.0433
37 H 7.3313 3.5147 0.4639 1 1 LIG1 0.0433
@<TRIPOS>BOND
1 1 2 1
2 1 22 1
3 1 23 1
4 1 24 1
5 2 3 1
6 2 25 1
7 2 26 1
8 3 7 ar
9 3 4 ar
10 4 5 ar
11 4 27 1
12 5 6 ar
13 5 28 1
14 6 7 ar
15 6 8 1
16 8 9 2
17 8 29 1
18 9 15 1
19 9 10 1
20 10 11 2
21 10 12 am
22 12 13 1
23 12 21 1
24 13 14 2
25 13 15 1
26 15 16 1
27 16 17 1
28 16 30 1
29 16 31 1
30 17 18 2
31 17 19 1
32 19 20 1
33 20 32 1
34 20 33 1
35 20 34 1
36 21 35 1
37 21 36 1
38 21 37 1
@<TRIPOS>MOLECULE
55 56 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C -8.0720 0.6252 -7.9328 C3 1 LIG1 -0.0494
2 C -8.4613 1.9045 -7.1893 C3 1 LIG1 0.0093
3 N -9.1610 1.5555 -5.9504 Npl 1 LIG1 -0.3304
4 C -10.6181 1.4039 -5.9499 C3 1 LIG1 0.0093
5 C -11.2710 2.7519 -5.6374 C3 1 LIG1 -0.0494
6 C -8.4421 1.3682 -4.7750 Car 1 LIG1 0.0297
7 C -9.1085 1.0366 -3.5985 Car 1 LIG1 -0.0399
8 C -8.3999 0.8506 -2.4336 Car 1 LIG1 -0.0478
9 C -7.0094 0.9945 -2.4326 Car 1 LIG1 0.0383
10 C -6.3436 1.3322 -3.6145 Car 1 LIG1 -0.0478
11 C -7.0574 1.5122 -4.7772 Car 1 LIG1 -0.0399
12 C -6.2467 0.7962 -1.1855 C2 1 LIG1 0.2601
13 O -6.8276 0.5074 -0.1570 O2 1 LIG1 -0.2687
14 N -4.9062 0.9353 -1.1860 Nam 1 LIG1 -0.2328
15 N -4.1819 0.7470 -0.0016 Npl 1 LIG1 -0.2686
16 C -2.8148 0.9920 0.0229 C2 1 LIG1 0.0188
17 C -2.2255 1.2932 -1.1017 C2 1 LIG1 -0.0601
18 C -0.7599 1.5918 -1.2259 C3 1 LIG1 -0.0149
19 C -0.0129 1.0877 0.0108 C3 1 LIG1 -0.0414
20 C -0.7406 1.5927 1.2629 C3 1 LIG1 -0.0379
21 H -0.8866 2.6706 1.1920 1 1 LIG1 0.0302
22 C -2.1043 0.8947 1.3413 C3 1 LIG1 -0.0110
23 C 0.0868 1.2625 2.5068 C3 1 LIG1 -0.0621
24 C -0.5595 3.1028 -1.3586 C3 1 LIG1 -0.0563
25 C -0.2048 0.8981 -2.4715 C3 1 LIG1 -0.0563
26 H -7.5514 0.8848 -8.8546 1 1 LIG1 0.0245
27 H -7.4170 0.0237 -7.3027 1 1 LIG1 0.0245
28 H -8.9704 0.0558 -8.1710 1 1 LIG1 0.0245
29 H -9.1163 2.5060 -7.8195 1 1 LIG1 0.0461
30 H -7.5629 2.4739 -6.9511 1 1 LIG1 0.0461
31 H -10.9479 1.0589 -6.9299 1 1 LIG1 0.0461
32 H -10.9074 0.6757 -5.1921 1 1 LIG1 0.0461
33 H -10.9818 3.4800 -6.3952 1 1 LIG1 0.0245
34 H -12.3552 2.6390 -5.6371 1 1 LIG1 0.0245
35 H -10.9413 3.0968 -4.6574 1 1 LIG1 0.0245
36 H -10.1828 0.9256 -3.6000 1 1 LIG1 0.0636
37 H -8.9175 0.5941 -1.5211 1 1 LIG1 0.0626
38 H -5.2699 1.4481 -3.6160 1 1 LIG1 0.0626
39 H -6.5433 1.7695 -5.6914 1 1 LIG1 0.0636
40 H -4.4428 1.1657 -2.0064 1 1 LIG1 0.1730
41 H -4.6351 0.4456 0.8013 1 1 LIG1 0.1696
42 H -2.8285 1.3296 -1.9969 1 1 LIG1 0.0593
43 H 0.0024 -0.0022 0.0105 1 1 LIG1 0.0276
44 H 1.0085 1.4683 0.0022 1 1 LIG1 0.0276
45 H -2.7091 1.3699 2.1136 1 1 LIG1 0.0328
46 H -1.9544 -0.1548 1.5944 1 1 LIG1 0.0328
47 H 1.0608 1.7465 2.4344 1 1 LIG1 0.0233
48 H -0.4327 1.6225 3.3948 1 1 LIG1 0.0233
49 H 0.2218 0.1832 2.5773 1 1 LIG1 0.0233
50 H 0.5035 3.3207 -1.4611 1 1 LIG1 0.0238
51 H -1.0910 3.4638 -2.2391 1 1 LIG1 0.0238
52 H -0.9484 3.6002 -0.4701 1 1 LIG1 0.0238
53 H -0.3402 -0.1794 -2.3781 1 1 LIG1 0.0238
54 H -0.7357 1.2559 -3.3536 1 1 LIG1 0.0238
55 H 0.8570 1.1236 -2.5702 1 1 LIG1 0.0238
@<TRIPOS>BOND
1 1 2 1
2 1 26 1
3 1 27 1
4 1 28 1
5 2 3 1
6 2 29 1
7 2 30 1
8 3 4 1
9 3 6 1
10 4 5 1
11 4 31 1
12 4 32 1
13 5 33 1
14 5 34 1
15 5 35 1
16 6 11 ar
17 6 7 ar
18 7 8 ar
19 7 36 1
20 8 9 ar
21 8 37 1
22 9 10 ar
23 9 12 1
24 10 11 ar
25 10 38 1
26 11 39 1
27 12 13 2
28 12 14 am
29 14 15 1
30 14 40 1
31 15 16 1
32 15 41 1
33 16 22 1
34 16 17 2
35 17 18 1
36 17 42 1
37 18 19 1
38 18 24 1
39 18 25 1
40 19 20 1
41 19 43 1
42 19 44 1
43 20 21 1
44 20 22 1
45 20 23 1
46 22 45 1
47 22 46 1
48 23 47 1
49 23 48 1
50 23 49 1
51 24 50 1
52 24 51 1
53 24 52 1
54 25 53 1
55 25 54 1
56 25 55 1
@<TRIPOS>MOLECULE
39 40 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 0.0021 -0.0041 0.0020 C3 1 LIG1 -0.0455
2 C -0.0187 1.5258 0.0104 C3 1 LIG1 0.0387
3 N -0.7044 1.9982 1.2158 Nar 1 LIG1 -0.2707
4 C -0.1980 2.8468 2.1248 Car 1 LIG1 0.0379
5 C -1.1606 3.0341 3.0965 Car 1 LIG1 0.0773
6 C -2.2770 2.2471 2.7348 Car 1 LIG1 0.0721
7 N -1.9953 1.6365 1.6169 Nar 1 LIG1 -0.1757
8 C -3.5668 2.1327 3.5056 C3 1 LIG1 -0.0199
9 C -1.0433 3.8899 4.2911 C2 1 LIG1 0.2516
10 O -1.9672 3.9649 5.0785 O2 1 LIG1 -0.2697
11 N 0.0877 4.5891 4.5107 Nam 1 LIG1 -0.2783
12 C 0.1994 5.4036 5.6477 Car 1 LIG1 0.0841
13 C -0.7358 5.6009 6.6147 Car 1 LIG1 0.0475
14 N -0.1986 6.4599 7.5189 Nar 1 LIG1 -0.2692
15 N 0.9870 6.7986 7.1592 Nar 1 LIG1 -0.1646
16 C 1.3098 6.2005 6.0286 Car 1 LIG1 0.1679
17 C 2.5846 6.3344 5.2987 C2 1 LIG1 0.2635
18 O 2.7580 5.7246 4.2611 O2 1 LIG1 -0.2686
19 N 3.5572 7.1325 5.7820 Nam 1 LIG1 -0.3240
20 C -0.8761 6.9365 8.7272 C3 1 LIG1 0.0388
21 C -0.0035 6.6454 9.9497 C3 1 LIG1 -0.0455
22 H 0.5293 -0.3651 0.8851 1 1 LIG1 0.0247
23 H -1.0205 -0.3814 0.0098 1 1 LIG1 0.0247
24 H 0.5123 -0.3556 -0.8948 1 1 LIG1 0.0247
25 H 1.0039 1.9031 0.0027 1 1 LIG1 0.0506
26 H -0.5459 1.8868 -0.8726 1 1 LIG1 0.0506
27 H 0.7814 3.3012 2.0993 1 1 LIG1 0.0834
28 H -3.4913 1.3136 4.2208 1 1 LIG1 0.0293
29 H -3.7552 3.0645 4.0390 1 1 LIG1 0.0293
30 H -4.3869 1.9373 2.8147 1 1 LIG1 0.0293
31 H 0.8246 4.5292 3.8827 1 1 LIG1 0.1552
32 H -1.7191 5.1564 6.6571 1 1 LIG1 0.0845
33 H 3.4189 7.6189 6.6097 1 1 LIG1 0.1453
34 H 4.3955 7.2205 5.3020 1 1 LIG1 0.1453
35 H -1.0455 8.0105 8.6491 1 1 LIG1 0.0506
36 H -1.8326 6.4246 8.8333 1 1 LIG1 0.0506
37 H 0.1659 5.5715 10.0278 1 1 LIG1 0.0247
38 H 0.9530 7.1573 9.8436 1 1 LIG1 0.0247
39 H -0.5076 7.0001 10.8487 1 1 LIG1 0.0247
@<TRIPOS>BOND
1 1 2 1
2 1 22 1
3 1 23 1
4 1 24 1
5 2 3 1
6 2 25 1
7 2 26 1
8 3 7 ar
9 3 4 ar
10 4 5 ar
11 4 27 1
12 5 6 ar
13 5 9 1
14 6 7 ar
15 6 8 1
16 8 28 1
17 8 29 1
18 8 30 1
19 9 10 2
20 9 11 am
21 11 12 1
22 11 31 1
23 12 16 ar
24 12 13 ar
25 13 14 ar
26 13 32 1
27 14 15 ar
28 14 20 1
29 15 16 ar
30 16 17 1
31 17 18 2
32 17 19 am
33 19 33 1
34 19 34 1
35 20 21 1
36 20 35 1
37 20 36 1
38 21 37 1
39 21 38 1
40 21 39 1
You would want something like this:
with open('old_file.txt') as in_file:
with open('new_file.txt, 'w') as out_file:
for line in old_file:
new_file.write(line)
if new_file.startswith('@<TRIPOS>MOLECULE'):
new_file.write('MOLECULE NAME')
I like generators (tested code here)
import itertools as itt
import os
import sys
def gen_names():
for cnt in itt.count(1):
yield 'MOLECULE{}'.format(cnt)
def augmented_lines(line_seq, name_seq):
name_seq = iter(name_seq)
for line in line_seq:
yield line
if line.startswith('@<TRIPOS>MOLECULE'):
yield next(name_seq) + '\n'
if __name__ == '__main__':
src_fn = os.path.join(os.path.dirname(__file__), 'five-molecules.txt')
with open(src_fn) as infile:
sys.stdout.writelines(augmented_lines(infile, gen_names()))