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Update README.md
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Qinqing Liu committed Nov 17, 2020
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Expand Up @@ -6,7 +6,7 @@ This is the code repository for OctSurf: Efficient Hierarchical Voxel-based Mole

## Experiments

### PDBbind Download
### Download PDBbind
Download PDBbind general, refined, and core(CASF) from http://www.pdbbind.org.cn.
And fix some minor problems(replace several mol2 files by transforming sdf in general set, and remove the CONECT with index 0 pdb file).
```angular2
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cd ..
```

### Set-up enviroment
### Set-up Enviroment
Install packages and compile the required tools, e.g. the java tool for generating surface points, the C++ code for octree, and the operation (convolution etc.) API for tensorflow.
```angular2
# compile java
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python octree_parse.py
cd ../
```
### CNN modeling
### CNN Modeling
#### prepare the data for modeling
First it will generate the points file for each complex in general, refined, core set. (The density of points can be specificed, low resolution OctSurf can use low density points to accelerate the process, here for depth=6 model, we use density 3. Can be specified in .sh file)
Then the points and labels will be transformed into tfrecords file.
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