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Fix random rotations
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@NiklasKappel
NiklasKappel committed Apr 25, 2024
1 parent 3f3bb86 commit 27bee74
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Showing 3 changed files with 168 additions and 65 deletions.
4 changes: 3 additions & 1 deletion examples/create_o2_box.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
from molbox import Box, MolBox
from molbox.lammps_data import write_lammps_data
from molbox.rdkit_3d_ops import create_3d_mol_from_smiles, rotate_mol
from rdkit import Chem
from scipy.spatial.transform import Rotation


Expand All @@ -10,9 +11,10 @@ def main():
o2_mol = create_3d_mol_from_smiles("O=O")
num_mols = 32
for _ in range(num_mols):
rotation = Rotation.random(random_state=42)
rotation = Rotation.random()
new_mol = rotate_mol(o2_mol, rotation, "COM")
o2_box.add_mol_randomly(new_mol)
Chem.MolToMolFile(o2_box.mol, "examples/o2_box.mol")
write_lammps_data(o2_box, "examples/o2_box.lmpdat")


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128 changes: 64 additions & 64 deletions examples/o2_box.lmpdat
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Expand Up @@ -22,70 +22,70 @@ Masses

Atoms

1 1 1 -0.82000 1.51000 5.87950 0.49750 # O
2 1 1 -0.82000 0.69680 5.17790 0.09060 # O
3 2 1 -0.82000 4.20060 3.43600 5.64340 # O
4 2 1 -0.82000 3.38740 2.73440 5.23650 # O
5 3 1 -0.82000 6.92550 2.54890 7.92870 # O
6 3 1 -0.82000 6.11230 1.84730 7.52180 # O
7 4 1 -0.82000 1.04960 2.04430 9.01030 # O
8 4 1 -0.82000 0.23630 1.34270 8.60340 # O
9 5 1 -0.82000 9.82850 6.71930 5.19770 # O
10 5 1 -0.82000 9.01520 6.01770 4.79080 # O
11 6 1 -0.82000 4.89740 9.03610 9.23920 # O
12 6 1 -0.82000 4.08410 8.33460 8.83230 # O
13 7 1 -0.82000 5.28020 1.04250 1.29220 # O
14 7 1 -0.82000 4.46700 0.34100 0.88530 # O
15 8 1 -0.82000 8.04630 1.41080 6.04210 # O
16 8 1 -0.82000 7.23300 0.70930 5.63520 # O
17 9 1 -0.82000 5.51180 2.00770 8.04880 # O
18 9 1 -0.82000 4.69850 1.30610 7.64190 # O
19 10 1 -0.82000 5.38230 7.34780 8.09130 # O
20 10 1 -0.82000 4.56900 6.64630 7.68440 # O
21 11 1 -0.82000 5.89290 5.20160 1.83530 # O
22 11 1 -0.82000 5.07960 4.50000 1.42840 # O
23 12 1 -0.82000 9.83060 9.62740 3.23710 # O
24 12 1 -0.82000 9.01730 8.92580 2.83020 # O
25 13 1 -0.82000 5.29960 4.79080 8.92640 # O
26 13 1 -0.82000 4.48630 4.08920 8.51950 # O
27 14 1 -0.82000 2.50350 3.92090 8.77710 # O
28 14 1 -0.82000 1.69030 3.21940 8.37020 # O
29 15 1 -0.82000 7.28740 7.11910 1.97060 # O
30 15 1 -0.82000 6.47410 6.41760 1.56370 # O
31 16 1 -0.82000 1.65600 2.75270 0.93320 # O
32 16 1 -0.82000 0.84280 2.05110 0.52630 # O
33 17 1 -0.82000 8.21960 8.82360 2.02200 # O
34 17 1 -0.82000 7.40640 8.12200 1.61500 # O
35 18 1 -0.82000 9.95430 8.25970 7.03280 # O
36 18 1 -0.82000 9.14100 7.55810 6.62590 # O
37 19 1 -0.82000 7.72650 0.91710 8.71080 # O
38 19 1 -0.82000 6.91320 0.21550 8.30390 # O
39 20 1 -0.82000 7.42150 8.85070 6.34540 # O
40 20 1 -0.82000 6.60820 8.14910 5.93850 # O
41 21 1 -0.82000 5.06700 9.05260 9.11020 # O
42 21 1 -0.82000 4.25370 8.35100 8.70330 # O
43 22 1 -0.82000 1.91460 3.79480 2.25130 # O
44 22 1 -0.82000 1.10130 3.09330 1.84440 # O
45 23 1 -0.82000 8.16410 4.65750 2.33390 # O
46 23 1 -0.82000 7.35080 3.95600 1.92700 # O
47 24 1 -0.82000 4.00130 1.07330 1.79300 # O
48 24 1 -0.82000 3.18810 0.37170 1.38610 # O
49 25 1 -0.82000 6.39820 1.85540 5.68050 # O
50 25 1 -0.82000 5.58500 1.15380 5.27360 # O
51 26 1 -0.82000 7.76260 5.98560 9.63870 # O
52 26 1 -0.82000 6.94940 5.28400 9.23180 # O
53 27 1 -0.82000 6.21240 2.10670 0.49840 # O
54 27 1 -0.82000 5.39910 1.40520 0.09150 # O
55 28 1 -0.82000 3.63120 0.80060 9.20380 # O
56 28 1 -0.82000 2.81790 0.09900 8.79680 # O
57 29 1 -0.82000 4.87080 9.67330 1.89420 # O
58 29 1 -0.82000 4.05750 8.97170 1.48730 # O
59 30 1 -0.82000 1.81820 0.85510 6.82080 # O
60 30 1 -0.82000 1.00500 0.15350 6.41390 # O
61 31 1 -0.82000 4.86710 6.83020 6.40010 # O
62 31 1 -0.82000 4.05390 6.12860 5.99320 # O
63 32 1 -0.82000 4.71830 4.93120 9.63850 # O
64 32 1 -0.82000 3.90500 4.22960 9.23160 # O
1 1 1 -0.82000 6.90450 5.23720 6.49140 # O
2 1 1 -0.82000 7.10250 4.64310 5.52860 # O
3 2 1 -0.82000 2.38430 4.54550 1.62670 # O
4 2 1 -0.82000 1.46290 4.81410 0.99570 # O
5 3 1 -0.82000 8.47940 2.49120 2.42370 # O
6 3 1 -0.82000 8.30130 3.58670 2.71930 # O
7 4 1 -0.82000 2.11440 3.59610 7.71730 # O
8 4 1 -0.82000 1.01320 3.73940 7.42370 # O
9 5 1 -0.82000 2.85860 7.35000 5.82650 # O
10 5 1 -0.82000 2.55520 8.37580 6.24470 # O
11 6 1 -0.82000 4.01490 7.19160 9.32840 # O
12 6 1 -0.82000 4.16630 6.20020 8.76870 # O
13 7 1 -0.82000 1.54920 2.19380 6.35620 # O
14 7 1 -0.82000 2.27360 1.54400 6.96630 # O
15 8 1 -0.82000 3.19730 3.44040 5.82690 # O
16 8 1 -0.82000 2.38670 2.82430 6.35850 # O
17 9 1 -0.82000 2.96030 2.58010 6.05130 # O
18 9 1 -0.82000 2.79710 2.33920 4.94020 # O
19 10 1 -0.82000 9.71520 1.94650 0.99180 # O
20 10 1 -0.82000 9.44010 0.85010 1.19550 # O
21 11 1 -0.82000 3.06770 3.30350 8.54490 # O
22 11 1 -0.82000 2.73920 3.34820 9.64450 # O
23 12 1 -0.82000 6.48700 0.36360 7.19200 # O
24 12 1 -0.82000 5.87300 1.32990 7.28380 # O
25 13 1 -0.82000 8.88380 4.01260 4.02690 # O
26 13 1 -0.82000 8.53170 3.17830 3.32050 # O
27 14 1 -0.82000 1.36480 3.67210 8.92880 # O
28 14 1 -0.82000 1.73620 3.69300 7.84220 # O
29 15 1 -0.82000 0.78520 6.41470 3.69760 # O
30 15 1 -0.82000 0.31480 7.45150 3.84910 # O
31 16 1 -0.82000 0.57190 0.57620 8.20900 # O
32 16 1 -0.82000 1.14700 0.55780 9.20300 # O
33 17 1 -0.82000 8.36540 8.86050 5.54070 # O
34 17 1 -0.82000 8.77890 9.65910 4.82620 # O
35 18 1 -0.82000 5.10150 6.62530 2.94410 # O
36 18 1 -0.82000 5.98610 6.78410 3.65920 # O
37 19 1 -0.82000 4.75900 7.12220 4.34040 # O
38 19 1 -0.82000 4.46750 8.22350 4.19460 # O
39 20 1 -0.82000 7.34780 7.99790 4.84200 # O
40 20 1 -0.82000 7.24200 6.96390 4.35330 # O
41 21 1 -0.82000 3.25490 4.39510 5.21520 # O
42 21 1 -0.82000 2.33090 4.99370 5.54240 # O
43 22 1 -0.82000 7.92470 8.01840 0.80820 # O
44 22 1 -0.82000 7.93400 6.87390 0.71290 # O
45 23 1 -0.82000 6.22460 8.87810 6.48960 # O
46 23 1 -0.82000 6.50240 8.53260 5.43010 # O
47 24 1 -0.82000 4.02890 4.43300 7.49050 # O
48 24 1 -0.82000 2.92010 4.72160 7.41080 # O
49 25 1 -0.82000 6.66310 6.67840 7.61370 # O
50 25 1 -0.82000 5.91920 5.86720 7.94200 # O
51 26 1 -0.82000 9.51210 8.45910 7.02870 # O
52 26 1 -0.82000 8.92810 9.41000 6.75680 # O
53 27 1 -0.82000 9.15020 2.21150 5.52630 # O
54 27 1 -0.82000 9.07360 1.10950 5.84100 # O
55 28 1 -0.82000 9.40050 9.44570 1.91290 # O
56 28 1 -0.82000 9.26640 9.05630 0.84070 # O
57 29 1 -0.82000 8.30820 1.24210 6.11150 # O
58 29 1 -0.82000 8.25310 1.66800 7.17680 # O
59 30 1 -0.82000 5.85860 9.61010 1.51910 # O
60 30 1 -0.82000 6.85080 9.21020 1.93750 # O
61 31 1 -0.82000 9.51230 4.02790 0.12790 # O
62 31 1 -0.82000 8.80700 3.36600 0.74730 # O
63 32 1 -0.82000 6.64700 1.76700 5.62250 # O
64 32 1 -0.82000 6.26970 0.70250 5.41330 # O


Bonds
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101 changes: 101 additions & 0 deletions examples/o2_box.mol
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RDKit 3D

64 32 0 0 0 0 0 0 0 0999 V2000
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M END

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