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add unimol docking v2 (#222)
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Co-authored-by: zhougm <[email protected]>
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@ZhouGengmo
ZhouGengmo and zhougm authored May 15, 2024
1 parent 3997c1c commit 6b9a780
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9 changes: 9 additions & 0 deletions unimol_docking_v2/README.md
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Uni-Mol Docking V2
===================================================================


Dependencies
------------
- [Uni-Core](https://github.com/dptech-corp/Uni-Core), check its [Installation Documentation](https://github.com/dptech-corp/Uni-Core#installation).
- rdkit==2022.9.3, install via `pip install rdkit-pypi==2022.9.3 -i https://pypi.tuna.tsinghua.edu.cn/simple/ --trusted-host pypi.tuna.tsinghua.edu.cn`
- biopandas==0.4.1, install via `pip install biopandas`
10 changes: 10 additions & 0 deletions unimol_docking_v2/docker/Dockerfile
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FROM dptechnology/unicore:0.0.1-pytorch1.11.0-cuda11.3

RUN pip install rdkit-pypi==2022.9.3
RUN pip install biopandas

RUN ldconfig && \
apt-get clean && \
apt-get autoremove && \
rm -rf /var/lib/apt/lists/* /tmp/* && \
conda clean -ya
30 changes: 30 additions & 0 deletions unimol_docking_v2/example_data/dict_mol.txt
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[PAD]
[CLS]
[SEP]
[UNK]
C
N
O
S
H
Cl
F
Br
I
Si
P
B
Na
K
Al
Ca
Sn
As
Hg
Fe
Zn
Cr
Se
Gd
Au
Li
9 changes: 9 additions & 0 deletions unimol_docking_v2/example_data/dict_pkt.txt
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[PAD]
[CLS]
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[UNK]
C
N
O
S
H
8 changes: 8 additions & 0 deletions unimol_docking_v2/example_data/docking_grid.json
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{
"center_x": 8.728845596313477,
"center_y": 25.618770599365234,
"center_z": 4.682269096374512,
"size_x": 19.121000289916992,
"size_y": 16.562999725341797,
"size_z": 18.64900016784668
}
167 changes: 167 additions & 0 deletions unimol_docking_v2/example_data/ligand.sdf
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1a30_ligand
RDKit 3D

49 48 0 0 0 0 0 0 0 0999 V2000
4.8410 27.5760 5.3100 N 0 0 0 0 0 0 0 0 0 0 0 0
5.7330 26.3940 5.1650 C 0 0 2 0 0 0 0 0 0 0 0 0
7.1740 26.7720 5.5040 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6240 27.8870 5.2180 O 0 0 0 0 0 0 0 0 0 0 0 0
5.6380 25.8180 3.7500 C 0 0 1 0 0 0 0 0 0 0 0 0
5.8270 26.8460 2.6520 C 0 0 1 0 0 0 0 0 0 0 0 0
5.6250 26.2750 1.2620 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6630 25.4970 1.0650 O 0 0 0 0 0 0 0 0 0 0 0 0
6.4250 26.6200 0.3630 O 0 0 0 0 0 0 0 0 0 0 0 0
7.8730 25.8560 6.1630 N 0 0 0 0 0 0 0 0 0 0 0 0
9.2580 26.0720 6.5600 C 0 0 1 0 0 0 0 0 0 0 0 0
10.1010 24.9180 6.0470 C 0 0 0 0 0 0 0 0 0 0 0 0
10.1820 23.8640 6.6820 O 0 0 0 0 0 0 0 0 0 0 0 0
9.3460 26.1960 8.0790 C 0 0 2 0 0 0 0 0 0 0 0 0
8.6490 27.4410 8.5880 C 0 0 0 0 0 0 0 0 0 0 0 0
9.2700 28.5180 8.5210 O 0 0 0 0 0 0 0 0 0 0 0 0
7.4740 27.3570 9.0120 O 0 0 0 0 0 0 0 0 0 0 0 0
10.6860 25.1150 4.8690 N 0 0 0 0 0 0 0 0 0 0 0 0
11.4980 24.0930 4.2260 C 0 0 2 0 0 0 0 0 0 0 0 0
12.9840 24.3990 4.2680 C 0 0 0 0 0 0 0 0 0 0 0 0
13.7840 23.4420 4.1920 O 0 0 0 0 0 0 0 0 0 0 0 0
11.0380 23.9220 2.7850 C 0 0 1 0 0 0 0 0 0 0 0 0
9.5830 23.4660 2.7700 C 0 0 2 0 0 0 0 0 0 0 0 0
8.8190 24.1970 1.7080 C 0 0 0 0 0 0 0 0 0 0 0 0
9.5210 21.9550 2.6020 C 0 0 0 0 0 0 0 0 0 0 0 0
13.3340 25.5920 4.3780 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 27 1 0
1 28 1 0
1 29 1 0
2 3 1 0
2 5 1 0
2 30 1 1
3 4 2 0
3 10 1 0
5 6 1 0
5 31 1 1
5 32 1 0
6 7 1 0
6 33 1 6
6 34 1 0
7 8 1 0
7 9 2 0
10 11 1 0
10 35 1 0
11 12 1 0
11 14 1 0
11 36 1 6
12 13 2 0
12 18 1 0
14 15 1 0
14 37 1 6
14 38 1 0
15 16 1 0
15 17 2 0
18 19 1 0
18 39 1 0
19 20 1 0
19 22 1 0
19 40 1 1
20 26 1 0
20 21 2 0
22 23 1 0
22 41 1 6
22 42 1 0
23 25 1 0
23 24 1 0
23 43 1 1
24 44 1 0
24 45 1 0
24 46 1 0
25 47 1 0
25 48 1 0
25 49 1 0
M CHG 4 1 1 8 -1 16 -1 26 -1
M END
> <name> (1)
1a30_ligand

> <fragInfo> (1)
11
1 49 49 49
7 8 9
6
5
2
3 4 10 49
20 21 26
23 24 25
22
19
12 13 18 49
15 16 17
14

> <torsionInfo> (1)
11 10 0 6
3 2 6 5
2 1 5 1
2 5 5 4
5 6 4 3
6 7 3 2
11 12 0 11
18 19 11 10
19 20 10 7
19 22 10 9
22 23 9 8
11 14 0 13
14 15 13 12

> <atomInfo> (1)
11 0 C
3 0 C
4 0 OA
10 0 N
49 0 HD
2 0 C
1 0 N
5 0 C
6 0 C
7 0 C
8 0 OA
9 0 OA
12 0 C
13 0 OA
18 0 N
19 0 C
20 0 C
21 0 OA
26 0 OA
22 0 C
23 0 C
24 0 C
25 0 C
14 0 C
15 0 C
16 0 OA
17 0 OA

$$$$
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