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add package version
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Qinqing Liu committed Aug 5, 2021
1 parent 087cec9 commit b9be5f6
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6 changes: 3 additions & 3 deletions README.md
Expand Up @@ -26,13 +26,13 @@ cd ../..
# set-up TF enviroment and compile cpp
conda create -n OctSurf_env tensorflow-gpu==1.14.0
conda activate OctSurf_env
conda install -c conda-forge openbabel
conda install -c conda-forge openbabel==3.0.0
conda install -c conda-forge yacs tqdm
pip install sklearn
pip install matplotlib
pip install seaborn
# uncomment if want to visualize in Paraview
# pip install vtk
# pip install vtk==9.0.3
cd octree/external && git clone --recursive https://github.com/wang-ps/octree-ext.git
Expand Down Expand Up @@ -82,7 +82,7 @@ python run_cls.py --config configs/train_resnet_depth6.yaml
Specify the config files (the path for pretrained model/test dataset, network architecture, iterations etc)
Test the pre-trained model on test dataset, and report the performance.
```angular2
python test_reg_ave.py --config configs/test_resnet_depth6.yaml
python test_reg_model.py --config configs/test_resnet_depth6.yaml
```

## Acknowledgments
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42 changes: 21 additions & 21 deletions pdbbind/python/utils.py
Expand Up @@ -670,27 +670,27 @@ def get_color_for_dep(depth, differ = True):
if differ == False:
color = 0
return color
if depth == 0:
color = 0 #[0, 0, 0] # white
elif depth == 1:
color = 1 # [255, 0, 0] # red
elif depth == 2:
color = 2 # [255, 128, 0]
elif depth == 3:
color = 3 #[255,255,0]
elif depth == 4:
color = 4 # [0, 255, 0]
elif depth == 5:
color = 5 #[0, 255, 255]
elif depth == 6:
color = 6 #[0, 0, 255]
elif depth == 7:
color = 7 # [255, 0 , 255]
elif depth == 8 :
color = 8
else:
color = 9
return color
# if depth == 0:
# color = 0 #[0, 0, 0] # white
# elif depth == 1:
# color = 1 # [255, 0, 0] # red
# elif depth == 2:
# color = 2 # [255, 128, 0]
# elif depth == 3:
# color = 3 #[255,255,0]
# elif depth == 4:
# color = 4 # [0, 255, 0]
# elif depth == 5:
# color = 5 #[0, 255, 255]
# elif depth == 6:
# color = 6 #[0, 0, 255]
# elif depth == 7:
# color = 7 # [255, 0 , 255]
# elif depth == 8 :
# color = 8
# else:
# color = 9
return depth

# A better way is use class in vtk package, this solve the color issue to distinguish ligand, pocket.
def vtk_writer(vtk_dic, file_name, shift = [0,0,0]):
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2 changes: 1 addition & 1 deletion tensorflow/script/test_reg_model.py
Expand Up @@ -28,5 +28,5 @@ def check_input(dataset='test', training=False, reuse=False, task = 'class'):
# solver = TFSolver(FLAGS.SOLVER, check_input)
# solver.check_grids()

solver = TFSolver(FLAGS.SOLVER, get_output)
solver = TFSolver(FLAGS, get_output)
solver.test_ave()

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