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Commit 1d695d4d authored by Jacob Durrant's avatar Jacob Durrant
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Added javascript-relevant code.

parent c70e2963
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.gitignore
View file @ 1d695d4d
**/*.pyc
**/__pycache__
.ipynb_checkpoints
old
data/**
!data/README.md
......
javascript_grid_gen/1b6l/1b6l_ligand.mol2 0 → 100755
View file @ 1d695d4d
###
### Created by X-TOOL on Mon Sep 10 21:12:47 2018
###
@<TRIPOS>MOLECULE
1b6l_ligand
83 85 1 0 0
SMALL
GAST_HUCK
@<TRIPOS>ATOM
1 C1 6.1160 2.8190 8.8070 C.3 1 PI4 -0.0084
2 C2 4.2430 3.2310 10.4450 C.2 1 PI4 0.1784
3 O3 4.1710 4.1370 11.2750 O.2 1 PI4 -0.3969
4 C4 4.7890 3.4970 9.0560 C.3 1 PI4 0.0398
5 N5 3.8770 1.9790 10.7050 N.am 1 PI4 -0.2635
6 C6 3.3110 1.5880 12.0060 C.3 1 PI4 0.1474
7 C7 3.9670 0.3640 12.6350 C.2 1 PI4 0.2045
8 O8 3.9310 -0.7320 12.0750 O.2 1 PI4 -0.3943
9 C9 1.8140 1.3240 11.8550 C.3 1 PI4 0.0773
10 C10 1.0770 2.5020 11.2770 C.2 1 PI4 0.1780
11 O11 0.5120 3.3110 12.0060 O.2 1 PI4 -0.3970
12 N12 1.0980 2.6210 9.9530 N.am 1 PI4 -0.3007
13 N13 4.5560 0.5590 13.8100 N.am 1 PI4 -0.2774
14 C14 5.2190 -0.5330 14.5340 C.3 1 PI4 0.0809
15 C15 6.7350 -0.3200 14.5350 C.3 1 PI4 0.0015
16 C16 7.2100 0.4410 13.3290 C.ar 1 PI4 -0.0515
17 C17 7.3330 1.8230 13.3770 C.ar 1 PI4 -0.0687
18 C18 7.6760 2.5460 12.2630 C.ar 1 PI4 -0.0396
19 C19 7.4640 -0.2060 12.1200 C.ar 1 PI4 -0.0687
20 C20 7.8110 0.5160 10.9900 C.ar 1 PI4 -0.0396
21 C21 7.9150 1.8950 11.0740 C.ar 1 PI4 0.0840
22 O22 8.2220 2.6510 9.9710 O.3 1 PI4 -0.3223
23 C23 7.2420 3.5620 9.5120 C.3 1 PI4 0.0710
24 C24 4.6850 -0.6120 15.9760 C.3 1 PI4 0.1192
25 O25 5.0950 0.5410 16.7170 O.3 1 PI4 -0.3841
26 C26 5.1720 -1.8710 16.6730 C.3 1 PI4 -0.0008
27 N27 4.4230 -3.0340 16.1410 N.4 1 PI4 0.2560
28 C28 5.1850 -4.2660 16.4870 C.3 1 PI4 0.0685
29 C29 4.4110 -5.5030 16.0160 C.3 1 PI4 0.0082
30 C30 2.9920 -5.5790 16.5630 C.3 1 PI4 -0.0410
31 C31 2.2510 -4.2800 16.2880 C.3 1 PI4 -0.0121
32 C32 3.0580 -3.0800 16.7610 C.3 1 PI4 -0.0297
33 C33 6.5680 -4.2310 15.8390 C.2 1 PI4 0.2251
34 O34 6.7200 -3.7110 14.7320 O.2 1 PI4 -0.3909
35 C35 8.9620 -4.8510 16.0860 C.3 1 PI4 0.0448
36 C36 9.4410 -3.4850 15.6080 C.3 1 PI4 -0.0396
37 C37 9.8500 -5.3020 17.2420 C.3 1 PI4 -0.0396
38 C38 9.0930 -5.8660 14.9560 C.3 1 PI4 -0.0396
39 N39 7.5630 -4.7800 16.5410 N.am 1 PI4 -0.2771
40 H1 6.0710 1.7876 9.1867 H 1 PI4 0.0315
41 H2 6.3158 2.8032 7.7254 H 1 PI4 0.0315
42 H3 4.0624 3.1289 8.3167 H 1 PI4 0.0503
43 H4 4.9204 4.5821 8.9323 H 1 PI4 0.0503
44 H5 3.9897 1.2831 9.9958 H 1 PI4 0.1884
45 H6 3.4509 2.4333 12.6958 H 1 PI4 0.0826
46 H7 1.3940 1.0967 12.8459 H 1 PI4 0.0551
47 H8 1.6735 0.4591 11.1900 H 1 PI4 0.0551
48 H9 0.6256 3.3841 9.5120 H 1 PI4 0.1814
49 H10 1.5862 1.9474 9.3981 H 1 PI4 0.1814
50 H11 4.5475 1.4745 14.2123 H 1 PI4 0.1857
51 H12 4.9970 -1.4818 14.0236 H 1 PI4 0.0604
52 H13 7.2293 -1.3026 14.5493 H 1 PI4 0.0428
53 H14 7.0116 0.2428 15.4387 H 1 PI4 0.0428
54 H15 7.1546 2.3405 14.3126 H 1 PI4 0.0530
55 H16 7.7585 3.6254 12.3187 H 1 PI4 0.0525
56 H17 7.3890 -1.2860 12.0639 H 1 PI4 0.0530
57 H18 7.9990 0.0081 10.0510 H 1 PI4 0.0525
58 H19 6.8306 4.1143 10.3697 H 1 PI4 0.0612
59 H20 7.7057 4.2693 8.8087 H 1 PI4 0.0612
60 H21 3.5859 -0.6357 15.9394 H 1 PI4 0.0672
61 H22 4.7253 0.5021 17.5912 H 1 PI4 0.2101
62 H23 4.9989 -1.7842 17.7558 H 1 PI4 0.0841
63 H24 6.2471 -2.0059 16.4832 H 1 PI4 0.0841
64 H25 4.3348 -2.9568 15.1398 H 1 PI4 0.2056
65 H26 5.3060 -4.3155 17.5792 H 1 PI4 0.1099
66 H27 4.9577 -6.4002 16.3417 H 1 PI4 0.0346
67 H28 4.3596 -5.4836 14.9174 H 1 PI4 0.0346
68 H29 3.0302 -5.7523 17.6486 H 1 PI4 0.0270
69 H30 2.4598 -6.4103 16.0775 H 1 PI4 0.0270
70 H31 1.2873 -4.2966 16.8181 H 1 PI4 0.0317
71 H32 2.0730 -4.1897 15.2063 H 1 PI4 0.0317
72 H33 2.5162 -2.1610 16.4929 H 1 PI4 0.0815
73 H34 3.1673 -3.1355 17.8541 H 1 PI4 0.0815
74 H35 10.4861 -3.5595 15.2731 H 1 PI4 0.0254
75 H36 9.3715 -2.7622 16.4343 H 1 PI4 0.0254
76 H37 8.8112 -3.1476 14.7717 H 1 PI4 0.0254
77 H38 10.8950 -5.3551 16.9025 H 1 PI4 0.0254
78 H39 9.5259 -6.2947 17.5877 H 1 PI4 0.0254
79 H40 9.7694 -4.5813 18.0691 H 1 PI4 0.0254
80 H41 10.1406 -5.9114 14.6236 H 1 PI4 0.0254
81 H42 8.4540 -5.5617 14.1139 H 1 PI4 0.0254
82 H43 8.7790 -6.8572 15.3151 H 1 PI4 0.0254
83 H44 7.3433 -5.1690 17.4357 H 1 PI4 0.1859
@<TRIPOS>BOND
1 1 23 1
2 1 4 1
3 4 2 1
4 2 5 am
5 2 3 2
6 5 6 1
7 6 9 1
8 6 7 1
9 7 13 am
10 7 8 2
11 13 14 1
12 14 24 1
13 14 15 1
14 15 16 1
15 16 19 ar
16 16 17 ar
17 17 18 ar
18 18 21 ar
19 21 22 1
20 21 20 ar
21 19 20 ar
22 23 22 1
23 24 26 1
24 24 25 1
25 26 27 1
26 27 32 1
27 27 28 1
28 28 33 1
29 28 29 1
30 29 30 1
31 30 31 1
32 32 31 1
33 33 39 am
34 33 34 2
35 39 35 1
36 35 38 1
37 35 37 1
38 35 36 1
39 9 10 1
40 10 12 am
41 10 11 2
42 1 40 1
43 1 41 1
44 4 42 1
45 4 43 1
46 5 44 1
47 6 45 1
48 9 46 1
49 9 47 1
50 12 48 1
51 12 49 1
52 13 50 1
53 14 51 1
54 15 52 1
55 15 53 1
56 17 54 1
57 18 55 1
58 19 56 1
59 20 57 1
60 23 58 1
61 23 59 1
62 24 60 1
63 25 61 1
64 26 62 1
65 26 63 1
66 27 64 1
67 28 65 1
68 29 66 1
69 29 67 1
70 30 68 1
71 30 69 1
72 31 70 1
73 31 71 1
74 32 72 1
75 32 73 1
76 36 74 1
77 36 75 1
78 36 76 1
79 37 77 1
80 37 78 1
81 37 79 1
82 38 80 1
83 38 81 1
84 38 82 1
85 39 83 1
@<TRIPOS>SUBSTRUCTURE
1 PI4 1
javascript_grid_gen/1b6l/1b6l_ligand.pdb 0 → 100644
View file @ 1d695d4d
HETATM 1 C UNL 1 6.116 2.819 8.807 1.00 0.00 C
HETATM 2 C UNL 1 4.243 3.231 10.445 1.00 0.00 C
HETATM 3 O UNL 1 4.171 4.137 11.275 1.00 0.00 O
HETATM 4 C UNL 1 4.789 3.497 9.056 1.00 0.00 C
HETATM 5 N UNL 1 3.877 1.979 10.705 1.00 0.00 N
HETATM 6 C UNL 1 3.311 1.588 12.006 1.00 0.00 C
HETATM 7 C UNL 1 3.967 0.364 12.635 1.00 0.00 C
HETATM 8 O UNL 1 3.931 -0.732 12.075 1.00 0.00 O
HETATM 9 C UNL 1 1.814 1.324 11.855 1.00 0.00 C
HETATM 10 C UNL 1 1.077 2.502 11.277 1.00 0.00 C
HETATM 11 O UNL 1 0.512 3.311 12.006 1.00 0.00 O
HETATM 12 N UNL 1 1.098 2.621 9.953 1.00 0.00 N
HETATM 13 N UNL 1 4.556 0.559 13.810 1.00 0.00 N
HETATM 14 C UNL 1 5.219 -0.533 14.534 1.00 0.00 C
HETATM 15 C UNL 1 6.735 -0.320 14.535 1.00 0.00 C
HETATM 16 C UNL 1 7.210 0.441 13.329 1.00 0.00 C
HETATM 17 C UNL 1 7.333 1.823 13.377 1.00 0.00 C
HETATM 18 C UNL 1 7.676 2.546 12.263 1.00 0.00 C
HETATM 19 C UNL 1 7.464 -0.206 12.120 1.00 0.00 C
HETATM 20 C UNL 1 7.811 0.516 10.990 1.00 0.00 C
HETATM 21 C UNL 1 7.915 1.895 11.074 1.00 0.00 C
HETATM 22 O UNL 1 8.222 2.651 9.971 1.00 0.00 O
HETATM 23 C UNL 1 7.242 3.562 9.512 1.00 0.00 C
HETATM 24 C UNL 1 4.685 -0.612 15.976 1.00 0.00 C
HETATM 25 O UNL 1 5.095 0.541 16.717 1.00 0.00 O
HETATM 26 C UNL 1 5.172 -1.871 16.673 1.00 0.00 C
HETATM 27 N UNL 1 4.423 -3.034 16.141 1.00 0.00 N1+
HETATM 28 C UNL 1 5.185 -4.266 16.487 1.00 0.00 C
HETATM 29 C UNL 1 4.411 -5.503 16.016 1.00 0.00 C
HETATM 30 C UNL 1 2.992 -5.579 16.563 1.00 0.00 C
HETATM 31 C UNL 1 2.251 -4.280 16.288 1.00 0.00 C
HETATM 32 C UNL 1 3.058 -3.080 16.761 1.00 0.00 C
HETATM 33 C UNL 1 6.568 -4.231 15.839 1.00 0.00 C
HETATM 34 O UNL 1 6.720 -3.711 14.732 1.00 0.00 O
HETATM 35 C UNL 1 8.962 -4.851 16.086 1.00 0.00 C
HETATM 36 C UNL 1 9.441 -3.485 15.608 1.00 0.00 C
HETATM 37 C UNL 1 9.850 -5.302 17.242 1.00 0.00 C
HETATM 38 C UNL 1 9.093 -5.866 14.956 1.00 0.00 C
HETATM 39 N UNL 1 7.563 -4.780 16.541 1.00 0.00 N
HETATM 40 H UNL 1 6.071 1.788 9.187 1.00 0.00 H
HETATM 41 H UNL 1 6.316 2.803 7.725 1.00 0.00 H
HETATM 42 H UNL 1 4.062 3.129 8.317 1.00 0.00 H
HETATM 43 H UNL 1 4.920 4.582 8.932 1.00 0.00 H
HETATM 44 H UNL 1 3.990 1.283 9.996 1.00 0.00 H
HETATM 45 H UNL 1 3.451 2.433 12.696 1.00 0.00 H
HETATM 46 H UNL 1 1.394 1.097 12.846 1.00 0.00 H
HETATM 47 H UNL 1 1.673 0.459 11.190 1.00 0.00 H
HETATM 48 H UNL 1 0.626 3.384 9.512 1.00 0.00 H
HETATM 49 H UNL 1 1.586 1.947 9.398 1.00 0.00 H
HETATM 50 H UNL 1 4.548 1.474 14.212 1.00 0.00 H
HETATM 51 H UNL 1 4.997 -1.482 14.024 1.00 0.00 H
HETATM 52 H UNL 1 7.229 -1.303 14.549 1.00 0.00 H
HETATM 53 H UNL 1 7.012 0.243 15.439 1.00 0.00 H
HETATM 54 H UNL 1 7.155 2.341 14.313 1.00 0.00 H
HETATM 55 H UNL 1 7.758 3.625 12.319 1.00 0.00 H
HETATM 56 H UNL 1 7.389 -1.286 12.064 1.00 0.00 H
HETATM 57 H UNL 1 7.999 0.008 10.051 1.00 0.00 H
HETATM 58 H UNL 1 6.831 4.114 10.370 1.00 0.00 H
HETATM 59 H UNL 1 7.706 4.269 8.809 1.00 0.00 H
HETATM 60 H UNL 1 3.586 -0.636 15.939 1.00 0.00 H
HETATM 61 H UNL 1 4.725 0.502 17.591 1.00 0.00 H
HETATM 62 H UNL 1 4.999 -1.784 17.756 1.00 0.00 H
HETATM 63 H UNL 1 6.247 -2.006 16.483 1.00 0.00 H
HETATM 64 H UNL 1 4.335 -2.957 15.140 1.00 0.00 H
HETATM 65 H UNL 1 5.306 -4.316 17.579 1.00 0.00 H
HETATM 66 H UNL 1 4.958 -6.400 16.342 1.00 0.00 H
HETATM 67 H UNL 1 4.360 -5.484 14.917 1.00 0.00 H
HETATM 68 H UNL 1 3.030 -5.752 17.649 1.00 0.00 H
HETATM 69 H UNL 1 2.460 -6.410 16.078 1.00 0.00 H
HETATM 70 H UNL 1 1.287 -4.297 16.818 1.00 0.00 H
HETATM 71 H UNL 1 2.073 -4.190 15.206 1.00 0.00 H
HETATM 72 H UNL 1 2.516 -2.161 16.493 1.00 0.00 H
HETATM 73 H UNL 1 3.167 -3.135 17.854 1.00 0.00 H
HETATM 74 H UNL 1 10.486 -3.559 15.273 1.00 0.00 H
HETATM 75 H UNL 1 9.371 -2.762 16.434 1.00 0.00 H
HETATM 76 H UNL 1 8.811 -3.148 14.772 1.00 0.00 H
HETATM 77 H UNL 1 10.895 -5.355 16.902 1.00 0.00 H
HETATM 78 H UNL 1 9.526 -6.295 17.588 1.00 0.00 H
HETATM 79 H UNL 1 9.769 -4.581 18.069 1.00 0.00 H
HETATM 80 H UNL 1 10.141 -5.911 14.624 1.00 0.00 H
HETATM 81 H UNL 1 8.454 -5.562 14.114 1.00 0.00 H
HETATM 82 H UNL 1 8.779 -6.857 15.315 1.00 0.00 H
HETATM 83 H UNL 1 7.343 -5.169 17.436 1.00 0.00 H
CONECT 1 23 4 40 41
CONECT 2 4 5 3
CONECT 3 2
CONECT 4 1 2 42 43
CONECT 5 2 6 44
CONECT 6 5 9 7 45
CONECT 7 6 13 8
CONECT 8 7
CONECT 9 6 10 46 47
CONECT 10 9 12 11
CONECT 11 10
CONECT 12 10 48 49
CONECT 13 7 14 50
CONECT 14 13 24 15 51
CONECT 15 14 16 52 53
CONECT 16 15 19 17
CONECT 17 16 18 54
CONECT 18 17 21 55
CONECT 19 16 20 56
CONECT 20 21 19 57
CONECT 21 18 22 20
CONECT 22 21 23
CONECT 23 1 22 58 59
CONECT 24 14 26 25 60
CONECT 25 24 61
CONECT 26 24 27 62 63
CONECT 27 26 32 28 64
CONECT 28 27 33 29 65
CONECT 29 28 30 66 67
CONECT 30 29 31 68 69
CONECT 31 30 32 70 71
CONECT 32 27 31 72 73
CONECT 33 28 39 34
CONECT 34 33
CONECT 35 39 38 37 36
CONECT 36 35 74 75 76
CONECT 37 35 77 78 79
CONECT 38 35 80 81 82
CONECT 39 33 35 83
CONECT 40 1
CONECT 41 1
CONECT 42 4
CONECT 43 4
CONECT 44 5
CONECT 45 6
CONECT 46 9
CONECT 47 9
CONECT 48 12
CONECT 49 12
CONECT 50 13
CONECT 51 14
CONECT 52 15
CONECT 53 15
CONECT 54 17
CONECT 55 18
CONECT 56 19
CONECT 57 20
CONECT 58 23
CONECT 59 23
CONECT 60 24
CONECT 61 25
CONECT 62 26
CONECT 63 26
CONECT 64 27
CONECT 65 28
CONECT 66 29
CONECT 67 29
CONECT 68 30
CONECT 69 30
CONECT 70 31
CONECT 71 31
CONECT 72 32
CONECT 73 32
CONECT 74 36
CONECT 75 36
CONECT 76 36
CONECT 77 37
CONECT 78 37
CONECT 79 37
CONECT 80 38
CONECT 81 38
CONECT 82 38
CONECT 83 39
MASTER 0 0 0 0 0 0 0 0 83 0 83 0
END
javascript_grid_gen/1b6l/1b6l_ligand.sdf 0 → 100755
View file @ 1d695d4d
1b6l_ligand
Created by X-TOOL on Fri Nov 18 12:37:04 2016
83 85 0 0 0 0 0 0 0 0999 V2000
6.1160 2.8190 8.8070 C 0 0 0 3 0 4
4.2430 3.2310 10.4450 C 0 0 0 1 0 3
4.1710 4.1370 11.2750 O 0 0 0 1 0 1
4.7890 3.4970 9.0560 C 0 0 0 3 0 4
3.8770 1.9790 10.7050 N 0 0 0 2 0 3
3.3110 1.5880 12.0060 C 0 0 0 2 0 4
3.9670 0.3640 12.6350 C 0 0 0 1 0 3
3.9310 -0.7320 12.0750 O 0 0 0 1 0 1
1.8140 1.3240 11.8550 C 0 0 0 3 0 4
1.0770 2.5020 11.2770 C 0 0 0 1 0 3
0.5120 3.3110 12.0060 O 0 0 0 1 0 1
1.0980 2.6210 9.9530 N 0 0 0 3 0 3
4.5560 0.5590 13.8100 N 0 0 0 2 0 3
5.2190 -0.5330 14.5340 C 0 0 0 2 0 4
6.7350 -0.3200 14.5350 C 0 0 0 3 0 4
7.2100 0.4410 13.3290 C 0 0 0 1 0 3
7.3330 1.8230 13.3770 C 0 0 0 2 0 3
7.6760 2.5460 12.2630 C 0 0 0 2 0 3
7.4640 -0.2060 12.1200 C 0 0 0 2 0 3
7.8110 0.5160 10.9900 C 0 0 0 2 0 3
7.9150 1.8950 11.0740 C 0 0 0 1 0 3
8.2220 2.6510 9.9710 O 0 0 0 1 0 2
7.2420 3.5620 9.5120 C 0 0 0 3 0 4
4.6850 -0.6120 15.9760 C 0 0 0 2 0 4
5.0950 0.5410 16.7170 O 0 0 0 2 0 2
5.1720 -1.8710 16.6730 C 0 0 0 3 0 4
4.4230 -3.0340 16.1410 N 0 3 0 2 0 4
5.1850 -4.2660 16.4870 C 0 0 0 2 0 4
4.4110 -5.5030 16.0160 C 0 0 0 3 0 4
2.9920 -5.5790 16.5630 C 0 0 0 3 0 4
2.2510 -4.2800 16.2880 C 0 0 0 3 0 4
3.0580 -3.0800 16.7610 C 0 0 0 3 0 4
6.5680 -4.2310 15.8390 C 0 0 0 1 0 3
6.7200 -3.7110 14.7320 O 0 0 0 1 0 1
8.9620 -4.8510 16.0860 C 0 0 0 1 0 4
9.4410 -3.4850 15.6080 C 0 0 0 4 0 4
9.8500 -5.3020 17.2420 C 0 0 0 4 0 4
9.0930 -5.8660 14.9560 C 0 0 0 4 0 4
7.5630 -4.7800 16.5410 N 0 0 0 2 0 3
6.0710 1.7876 9.1867 H 0 0 0 1 0 1
6.3158 2.8032 7.7254 H 0 0 0 1 0 1
4.0624 3.1289 8.3167 H 0 0 0 1 0 1
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3.9897 1.2831 9.9958 H 0 0 0 1 0 1
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1.3940 1.0967 12.8459 H 0 0 0 1 0 1
1.6735 0.4591 11.1900 H 0 0 0 1 0 1
0.6256 3.3841 9.5120 H 0 0 0 1 0 1
1.5862 1.9474 9.3981 H 0 0 0 1 0 1
4.5475 1.4745 14.2123 H 0 0 0 1 0 1
4.9970 -1.4818 14.0236 H 0 0 0 1 0 1
7.2293 -1.3026 14.5493 H 0 0 0 1 0 1
7.0116 0.2428 15.4387 H 0 0 0 1 0 1
7.1546 2.3405 14.3126 H 0 0 0 1 0 1
7.7585 3.6254 12.3187 H 0 0 0 1 0 1
7.3890 -1.2860 12.0639 H 0 0 0 1 0 1
7.9990 0.0081 10.0510 H 0 0 0 1 0 1
6.8306 4.1143 10.3697 H 0 0 0 1 0 1
7.7057 4.2693 8.8087 H 0 0 0 1 0 1
3.5859 -0.6357 15.9394 H 0 0 0 1 0 1
4.7253 0.5021 17.5912 H 0 0 0 1 0 1
4.9989 -1.7842 17.7558 H 0 0 0 1 0 1
6.2471 -2.0059 16.4832 H 0 0 0 1 0 1
4.3348 -2.9568 15.1398 H 0 0 0 1 0 1
5.3060 -4.3155 17.5792 H 0 0 0 1 0 1
4.9577 -6.4002 16.3417 H 0 0 0 1 0 1
4.3596 -5.4836 14.9174 H 0 0 0 1 0 1
3.0302 -5.7523 17.6486 H 0 0 0 1 0 1
2.4598 -6.4103 16.0775 H 0 0 0 1 0 1
1.2873 -4.2966 16.8181 H 0 0 0 1 0 1
2.0730 -4.1897 15.2063 H 0 0 0 1 0 1
2.5162 -2.1610 16.4929 H 0 0 0 1 0 1
3.1673 -3.1355 17.8541 H 0 0 0 1 0 1
10.4861 -3.5595 15.2731 H 0 0 0 1 0 1
9.3715 -2.7622 16.4343 H 0 0 0 1 0 1
8.8112 -3.1476 14.7717 H 0 0 0 1 0 1
10.8950 -5.3551 16.9025 H 0 0 0 1 0 1
9.5259 -6.2947 17.5877 H 0 0 0 1 0 1
9.7694 -4.5813 18.0691 H 0 0 0 1 0 1
10.1406 -5.9114 14.6236 H 0 0 0 1 0 1
8.4540 -5.5617 14.1139 H 0 0 0 1 0 1
8.7790 -6.8572 15.3151 H 0 0 0 1 0 1
7.3433 -5.1690 17.4357 H 0 0 0 1 0 1
1 23 1 0 0 1
1 4 1 0 0 1
4 2 1 0 0 1
2 5 1 0 0 1
2 3 2 0 0 2
5 6 1 0 0 1
6 9 1 0 0 2
6 7 1 0 0 1
7 13 1 0 0 1
7 8 2 0 0 2
13 14 1 0 0 1
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14 15 1 0 0 1
15 16 1 0 0 1
16 19 4 0 0 1
16 17 4 0 0 1
17 18 4 0 0 1
18 21 4 0 0 1
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21 20 4 0 0 1
19 20 4 0 0 1
23 22 1 0 0 1
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6 45 1 0 0 2
9 46 1 0 0 2
9 47 1 0 0 2
12 48 1 0 0 2
12 49 1 0 0 2
13 50 1 0 0 2
14 51 1 0 0 2
15 52 1 0 0 2
15 53 1 0 0 2
17 54 1 0 0 2
18 55 1 0 0 2
19 56 1 0 0 2
20 57 1 0 0 2
23 58 1 0 0 2
23 59 1 0 0 2
24 60 1 0 0 2
25 61 1 0 0 2
26 62 1 0 0 2
26 63 1 0 0 2
27 64 1 0 0 2
28 65 1 0 0 2
29 66 1 0 0 2
29 67 1 0 0 2
30 68 1 0 0 2
30 69 1 0 0 2
31 70 1 0 0 2
31 71 1 0 0 2
32 72 1 0 0 2
32 73 1 0 0 2
36 74 1 0 0 2
36 75 1 0 0 2
36 76 1 0 0 2
37 77 1 0 0 2
37 78 1 0 0 2
37 79 1 0 0 2
38 80 1 0 0 2
38 81 1 0 0 2
38 82 1 0 0 2
39 83 1 0 0 2
M END
> <MOLECULAR_FORMULA>
C28H44N5O6
> <MOLECULAR_WEIGHT>
546.3
> <NUM_HB_ATOMS>
11
> <NUM_ROTOR>
6
> <XLOGP2>
0.22
$$$$
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a
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Remember that all atoms in same layer. Good to divide by layer so you can
parallelize in browser.
Remember:
# __p_ragma__ ('js', "debugger")
DONE
====
remove hydrogen atoms
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javascript_grid_gen/__target__/gridder.fake_rdkit.js 0 → 100644
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'use strict';var re={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,__init__,__ior__,
__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,divmod,enumerate,
filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import*as __module_re__ from"./re.js";__nest__(re,"",__module_re__);var __name__="gridder.fake_rdkit";export var element_names_with_two_letters=["BR","CL","BI","AS","AG","LI","MG","RH","ZN","MN"];export var element_to_atomic_num=dict({"H":1,
"HE":2,"LI":3,"BE":4,"B":5,"C":6,"N":7,"O":8,"F":9,"NE":10,"NA":11,"MG":12,"AL":13,"SI":14,"P":15,"S":16,"CL":17,"AR":18,"K":19,"CA":20});export var Point=__class__("Point",[object],{__module__:__name__,get __init__(){return __get__(this,function(self,coor){self.x=coor[0];self.y=coor[1];self.z=coor[2]})},get __getitem__(){return __get__(this,function(self,key){if(key==0)return self.x;if(key==1)return self.y;if(key==2)return self.z;return 0})}});export var Atom=__class__("Atom",[object],{__module__:__name__,
get __init__(){return __get__(this,function(self,coor,py_name,element,resname){self.coor=Point(coor);self.py_name=py_name;self.element=element;self.resname=resname})},get GetAtomicNum(){return __get__(this,function(self){return element_to_atomic_num[self.element]})}});export var Mol=__class__("Mol",[object],{__module__:__name__,get __init__(){return __get__(this,function(self){self.atoms=[]})},get add_atom(){return __get__(this,function(self,coor,py_name,element,resname){self.atoms.append(Atom(coor,
py_name,element,resname))})},get GetAtomWithIdx(){return __get__(this,function(self,i){return self.atoms[i]})},get GetNumAtoms(){return __get__(this,function(self){return len(self.atoms)})},get GetConformer(){return __get__(this,function(self){return self})},get GetAtomPosition(){return __get__(this,function(self,i){return self.atoms[i].coor})}});export var MolIterator=__class__("MolIterator",[object],{__module__:__name__,get __init__(){return __get__(this,function(self,mol){self.mols=[mol]})},get __iter__(){return __get__(this,
function(self){return self})},[Symbol.iterator](){return this.__iter__()},get __next__(){return __get__(this,function(self){if(len(self.mols)==0){var __except0__=StopIteration;__except0__.__cause__=null;throw __except0__;}return self.mols.py_pop()})},next:__jsUsePyNext__});export var Chem=__class__("Chem",[object],{__module__:__name__,get MolFromPDBFile(){return function(filetxt,sanitize){var mol=Mol();var lines_src=filetxt.py_split("\n");var lines=function(){var __accu0__=[];for(var l of lines_src)if(l.startswith("ATOM")||
l.startswith("HETATM"))__accu0__.append(l);return __accu0__}();var coors=function(){var __accu0__=[];for(var l of lines)__accu0__.append([float(l.__getslice__(30,38,1)),float(l.__getslice__(38,46,1)),float(l.__getslice__(46,54,1))]);return __accu0__}();var names=function(){var __accu0__=[];for(var l of lines)__accu0__.append(l.__getslice__(11,16,1).strip());return __accu0__}();var elements_prep=function(){var __accu0__=[];for(var n of names)__accu0__.append(n.upper().strip());return __accu0__}();
for(var [i,e]of enumerate(elements_prep)){for(var num of"0123456789")var e=e.py_replace(num,"");elements_prep[i]=e}var elements_prep=function(){var __accu0__=[];for(var e of elements_prep)__accu0__.append(e.__getslice__(0,2,1));return __accu0__}();var elements=[];for(var e of elements_prep)elements.append(Chem.name_to_element(e));var resnames=function(){var __accu0__=[];for(var l of lines)__accu0__.append(l.__getslice__(16,21,1).strip());return __accu0__}();for(var i=0;i<len(coors);i++)mol.add_atom(coors[i],
names[i],elements[i],resnames[i]);return mol}},get name_to_element(){return function(py_name){if(__in__(py_name,element_names_with_two_letters))return py_name;else return py_name.__getslice__(0,1,1)}},get SDMolSupplier(){return function(filetxt,sanitize){if(typeof sanitize=="undefined"||sanitize!=null&&sanitize.hasOwnProperty("__kwargtrans__"))var sanitize=false;var mol=Mol();var txt=filetxt;var atoms=re.findall("^ *?[\\-0-9]+?\\.[\\-0-9]+? *?[\\-0-9]+?\\.[\\-0-9]+? *?[\\-0-9]+?\\.[\\-0-9]+? *?[a-zA-Z]+? *?[\\-0-9]+? *?[\\-0-9]+? *?[\\-0-9]+? *?[\\-0-9]+? *?[\\-0-9]+? *?[\\-0-9]+? *?$",
txt,re.MULTILINE);var atoms=function(){var __accu0__=[];for(var a of atoms)__accu0__.append(a.strip().py_split().__getslice__(0,4,1));return __accu0__}();for(var [x,y,z,py_name]of atoms)mol.add_atom([float(x),float(y),float(z)],py_name,Chem.name_to_element(py_name),"");var py_iter=MolIterator(mol);return py_iter}}});
//# sourceMappingURL=gridder.fake_rdkit.map
\ No newline at end of file
javascript_grid_gen/__target__/gridder.grid_util.js 0 → 100644
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'use strict';var math={};var random={};import{AssertionError,AttributeError,BaseException,DeprecationWarning,Exception,IndexError,IterableError,KeyError,NotImplementedError,RuntimeWarning,StopIteration,UserWarning,ValueError,Warning,__JsIterator__,__PyIterator__,__Terminal__,__add__,__and__,__call__,__class__,__envir__,__eq__,__floordiv__,__ge__,__get__,__getcm__,__getitem__,__getslice__,__getsm__,__gt__,__i__,__iadd__,__iand__,__idiv__,__ijsmod__,__ilshift__,__imatmul__,__imod__,__imul__,__in__,
__init__,__ior__,__ipow__,__irshift__,__isub__,__ixor__,__jsUsePyNext__,__jsmod__,__k__,__kwargtrans__,__le__,__lshift__,__lt__,__matmul__,__mergefields__,__mergekwargtrans__,__mod__,__mul__,__ne__,__neg__,__nest__,__or__,__pow__,__pragma__,__proxy__,__pyUseJsNext__,__rshift__,__setitem__,__setproperty__,__setslice__,__sort__,__specialattrib__,__sub__,__super__,__t__,__terminal__,__truediv__,__withblock__,__xor__,abs,all,any,assert,bool,bytearray,bytes,callable,chr,copy,deepcopy,delattr,dict,dir,
divmod,enumerate,filter,float,getattr,hasattr,input,int,isinstance,issubclass,len,list,map,max,min,object,ord,pow,print,property,py_TypeError,py_iter,py_metatype,py_next,py_reversed,py_typeof,range,repr,round,set,setattr,sorted,str,sum,tuple,zip}from"./org.transcrypt.__runtime__.js";import{KDTree}from"./gridder.kdtrees._kdtree.js";import*as __module_random__ from"./random.js";__nest__(