add package version

README.md

@@ -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
@@ -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

pdbbind/python/utils.py

@@ -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]):

tensorflow/script/test_reg_model.py

@@ -28,5 +28,5 @@ if __name__ == '__main__':
   # solver = TFSolver(FLAGS.SOLVER, check_input)
   # solver.check_grids()
 
-  solver = TFSolver(FLAGS.SOLVER, get_output)
+  solver = TFSolver(FLAGS, get_output)
   solver.test_ave()