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Qinqing Liu committed Nov 16, 2020
1 parent 478d059 commit d80e6a9
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5 changes: 2 additions & 3 deletions README.md
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Expand Up @@ -58,19 +58,18 @@ cd ../

- prepare the data
```angular2
cd pdbbind
bash data_prepare_model.sh
cd ..
```
- train model
```angular2
cd tensorflow/script
python run_cls.py --config configs/vgg_depth6.yaml
python run_cls.py --config configs/train_resnet_depth6.yaml
```

- test performance
```angular2
python test_reg_ave.py --config configs/vgg_depth6_test.yaml
python test_reg_ave.py --config configs/test_resnet_depth6.yaml
```

### Acknowledgments
Expand Down
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6 changes: 6 additions & 0 deletions pdbbind/bash_scripts/correct_index0.sh
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for D in ./*/;
do
cd "${D}";
python ../../python/clean_index_error.py
cd ..;
done
13 changes: 13 additions & 0 deletions pdbbind/bash_scripts/correct_mol2.sh
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for D in '3qlb' '4oem' '4oel' '2fov' '2fou' '2foy'
do
cd "${D}";
echo "${D}";
FNAME=$(basename ${D})
FPATH=$(dirname ${D})
DNAME=$(basename ${FNAME})
echo $DNAME

mv ${DNAME}_ligand.mol2 ${DNAME}_ligand.mol2.record;
babel ${DNAME}_ligand.sdf -omol2 ${DNAME}_ligand.mol2;
cd ..
done
10 changes: 10 additions & 0 deletions pdbbind/bash_scripts/data_prepare_points.sh
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for D in ./*/;
do
echo "${D}";
cd "${D}";
java -cp ../../../java/cdk-2.3-SNAPSHOT.jar:../../../java Surface_for_single 3 ico pdbbind;
python ../../../python/write_complex.py
python ../../../python/atomic_feature.py
../../../../octree/build/pdb_to_points --complex_id file_list.txt
cd ..;
done
12 changes: 12 additions & 0 deletions pdbbind/bash_scripts/octree_for_single.sh
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# here 6 is a parameter to control the density of point clouds
# 6 is for depth 10, can try smaller numbers e.g. 3-5 for smaller depth
java -cp ../../../java/cdk-2.3-SNAPSHOT.jar:../../../java Surface_for_single 6 ico pdbbind

python ../../../python/write_complex.py
python ../../../python/atomic_feature.py
../../../../octree/build/pdb_to_points --complex_id file_list.txt
mkdir octree_folder
../../../../octree/build/octree --depth 10 --filenames point_list.txt --output_path ./octree_folder
cd octree_folder
ls -lh

27 changes: 27 additions & 0 deletions pdbbind/data_download.sh
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mkdir data_folder
cd data_folder

wget "http://www.pdbbind.org.cn/download/pdbbind_v2018_refined.tar.gz"
wget "http://www.pdbbind.org.cn/download/pdbbind_v2018_other_PL.tar.gz"
wget "http://www.pdbbind-cn.org/download/CASF-2016.tar.gz"

tar -xzvf pdbbind_v2018_refined.tar.gz
tar -xzvf pdbbind_v2018_other_PL.tar.gz
tar -xzvf CASF-2016.tar.gz
mv CASF-2016/coreset .

cp ../bash_scripts/* v2018-other-PL
cp ../bash_scripts/* refined-set
cp ../bash_scripts/* coreset

cd v2018-other-PL
bash correct_mol2.sh
bash correct_index0.sh

cd ../refined-set
bash correct_index0.sh

cd ../coreset
bash correct_index0.sh


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163 changes: 163 additions & 0 deletions pdbbind/data_example/pdbbind/1a1e/1a1e_ligand.mol2
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###
### Created by X-TOOL on Mon Sep 10 21:12:46 2018
###

@<TRIPOS>MOLECULE
1a1e_ligand
73 74 1 0 0
SMALL
GAST_HUCK


@<TRIPOS>ATOM
1 C 43.2930 -8.1280 37.5500 C.2 1 ACE 0.1753
2 O 44.0670 -7.1860 37.7880 O.2 1 ACE -0.3972
3 CH3 43.5190 -9.0100 36.3320 C.3 1 ACE 0.0258
4 N 42.1690 -8.3110 38.2080 N.am 1 PTR -0.2628
5 CA 41.8750 -7.5040 39.3540 C.3 1 PTR 0.1468
6 C 42.3970 -8.1890 40.5900 C.2 1 PTR 0.2074
7 O 42.8670 -9.3290 40.5910 O.2 1 PTR -0.3941
8 CB 40.3910 -7.2910 39.3740 C.3 1 PTR 0.0400
9 CG 40.0200 -6.4670 38.1650 C.ar 1 PTR -0.0004
10 CD1 39.4330 -7.0660 37.0710 C.ar 1 PTR -0.0239
11 CD2 40.2030 -5.0890 38.1630 C.ar 1 PTR -0.0239
12 CE1 39.0230 -6.2990 35.9910 C.ar 1 PTR 0.0115
13 CE2 39.7950 -4.3030 37.0800 C.ar 1 PTR 0.0115
14 CZ 39.1970 -4.9130 35.9920 C.ar 1 PTR 0.1728
15 OH 38.7140 -4.1030 34.8990 O.3 1 PTR -0.2040
16 P 39.5630 -3.9590 33.5410 P.3 1 PTR 0.1348
17 O1P 39.2960 -5.2230 32.8550 O.co2 1 PTR -0.6653
18 O2P 38.9860 -2.7290 32.9200 O.co2 1 PTR -0.6653
19 O3P 40.9750 -3.8330 34.0580 O.co2 1 PTR -0.6653
20 N 42.3460 -7.4520 41.6620 N.am 1 GLU -0.2634
21 CA 42.8210 -7.9260 42.9250 C.3 1 GLU 0.1325
22 C 41.6490 -8.4730 43.7280 C.2 1 GLU 0.2042
23 O 40.5250 -7.9950 43.5040 O.2 1 GLU -0.3943
24 CB 43.4630 -6.7590 43.6070 C.3 1 GLU -0.0008
25 CG 44.7130 -6.2540 42.9200 C.3 1 GLU 0.0044
26 CD 45.8500 -7.2030 43.1550 C.2 1 GLU 0.0350
27 OE1 46.3510 -7.2360 44.2790 O.co2 1 GLU -0.5690
28 OE2 46.2130 -7.9200 42.2380 O.co2 1 GLU -0.5690
29 N1 41.7710 -9.4590 44.6560 N.am 1 DIY -0.2711
30 C2 43.0100 -10.2080 44.8790 C.3 1 DIY 0.0340
31 C6 40.6720 -9.7740 45.5450 C.3 1 DIY 0.0368
32 C3 43.5030 -9.7480 46.2370 C.3 1 DIY -0.0322
33 C4 42.3970 -9.9440 47.2660 C.3 1 DIY -0.0465
34 C5 41.0210 -9.3410 46.9320 C.3 1 DIY -0.0205
35 C1' 40.9160 -7.8430 47.1120 C.3 1 DIY -0.0484
36 C2' 41.2000 -7.5140 48.5540 C.3 1 DIY -0.0530
37 C3' 41.5460 -6.0620 48.7310 C.3 1 DIY -0.0559
38 C4' 40.3430 -5.2830 48.3020 C.3 1 DIY -0.0653
39 H1 42.7378 -9.7833 36.2893 H 1 ACE 0.0467
40 H2 44.5062 -9.4898 36.4047 H 1 ACE 0.0467
41 H3 43.4764 -8.3951 35.4210 H 1 ACE 0.0467
42 H4 41.5214 -9.0118 37.9089 H 1 PTR 0.1885
43 H5 42.3738 -6.5282 39.2592 H 1 PTR 0.0840
44 H6 40.1031 -6.7573 40.2917 H 1 PTR 0.0584
45 H7 39.8744 -8.2614 39.3368 H 1 PTR 0.0584
46 H8 39.2914 -8.1406 37.0549 H 1 PTR 0.0703
47 H9 40.6711 -4.6140 39.0176 H 1 PTR 0.0703
48 H10 38.5622 -6.7805 35.1361 H 1 PTR 0.0736
49 H11 39.9456 -3.2296 37.0933 H 1 PTR 0.0736
50 H12 41.9644 -6.5297 41.6007 H 1 GLU 0.1883
51 H13 43.5632 -8.7244 42.7773 H 1 GLU 0.0801
52 H14 43.7293 -7.0606 44.6308 H 1 GLU 0.0330
53 H15 42.7334 -5.9367 43.6450 H 1 GLU 0.0330
54 H16 44.9755 -5.2649 43.3235 H 1 GLU 0.0433
55 H17 44.5259 -6.1712 41.8392 H 1 GLU 0.0433
56 H18 43.7496 -9.9743 44.0990 H 1 DIY 0.0522
57 H19 42.8127 -11.2901 44.8848 H 1 DIY 0.0522
58 H20 40.4890 -10.8586 45.5335 H 1 DIY 0.0525
59 H21 39.7665 -9.2458 45.2118 H 1 DIY 0.0525
60 H22 43.7750 -8.6833 46.1881 H 1 DIY 0.0285
61 H23 44.3843 -10.3387 46.5276 H 1 DIY 0.0285
62 H24 42.7373 -9.4929 48.2098 H 1 DIY 0.0269
63 H25 42.2605 -11.0266 47.4052 H 1 DIY 0.0269
64 H26 40.2896 -9.7888 47.6209 H 1 DIY 0.0320
65 H27 39.9023 -7.5076 46.8476 H 1 DIY 0.0269
66 H28 41.6493 -7.3392 46.4651 H 1 DIY 0.0269
67 H29 42.0448 -8.1273 48.9007 H 1 DIY 0.0265
68 H30 40.3083 -7.7446 49.1554 H 1 DIY 0.0265
69 H31 42.4119 -5.7988 48.1057 H 1 DIY 0.0263
70 H32 41.7780 -5.8525 49.7856 H 1 DIY 0.0263
71 H33 40.5443 -4.2072 48.4124 H 1 DIY 0.0230
72 H34 39.4832 -5.5613 48.9290 H 1 DIY 0.0230
73 H35 40.1170 -5.5076 47.2492 H 1 DIY 0.0230
@<TRIPOS>BOND
1 1 2 2
2 1 3 1
3 5 4 1
4 5 8 1
5 6 5 1
6 6 7 2
7 8 9 1
8 9 11 ar
9 9 10 ar
10 10 12 ar
11 12 14 ar
12 14 15 1
13 13 14 ar
14 11 13 ar
15 15 16 1
16 16 19 ar
17 16 18 ar
18 16 17 ar
19 22 21 1
20 21 24 1
21 21 20 1
22 24 25 1
23 25 26 1
24 26 27 ar
25 26 28 ar
26 22 23 2
27 29 31 1
28 29 30 1
29 30 32 1
30 32 33 1
31 34 33 1
32 34 35 1
33 31 34 1
34 35 36 1
35 36 37 1
36 37 38 1
37 4 1 am
38 20 6 am
39 22 29 am
40 3 39 1
41 3 40 1
42 3 41 1
43 4 42 1
44 5 43 1
45 8 44 1
46 8 45 1
47 10 46 1
48 11 47 1
49 12 48 1
50 13 49 1
51 20 50 1
52 21 51 1
53 24 52 1
54 24 53 1
55 25 54 1
56 25 55 1
57 30 56 1
58 30 57 1
59 31 58 1
60 31 59 1
61 32 60 1
62 32 61 1
63 33 62 1
64 33 63 1
65 34 64 1
66 35 65 1
67 35 66 1
68 36 67 1
69 36 68 1
70 37 69 1
71 37 70 1
72 38 71 1
73 38 72 1
74 38 73 1
@<TRIPOS>SUBSTRUCTURE
1 ACE 1

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