From b9be5f63b6b29e063f9f9812305f605ba872fcca Mon Sep 17 00:00:00 2001
From: Qinqing Liu <liuqinqing94@gmail.com>
Date: Thu, 5 Aug 2021 14:42:43 -0400
Subject: [PATCH] add package version

---
 .DS_Store                           | Bin 10244 -> 10244 bytes
 README.md                           |   6 ++--
 octree/.DS_Store                    | Bin 10244 -> 10244 bytes
 pdbbind/.DS_Store                   | Bin 8196 -> 8196 bytes
 pdbbind/python/utils.py             |  42 ++++++++++++++--------------
 tensorflow/.DS_Store                | Bin 10244 -> 10244 bytes
 tensorflow/script/.DS_Store         | Bin 10244 -> 10244 bytes
 tensorflow/script/test_reg_model.py |   2 +-
 8 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index 85af8d6c52980bc6a2af9f3ad261c321b82099b5..6d64b5fecb68f528f2bd6bd0871fb22834317563 100644
GIT binary patch
delta 265
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Ii83<-00tgM8UO$Q

delta 271
zcmZn(XbIS$CJ?(;f`Ng7g+Y%YogtH<Bsbs1B`GIA2`I+V?)&g(?&d>|sPZXz<qI+l
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Kv1}4$W(EM)zDzj)

diff --git a/README.md b/README.md
index 34c6c42..3b1144b 100644
--- a/README.md
+++ b/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
diff --git a/octree/.DS_Store b/octree/.DS_Store
index 54d263c8d76a4e665667c4a25290399d2249cfb2..24bba19c8529283e66482fb06056fe3fa74442f2 100644
GIT binary patch
delta 191
zcmV;w06_nQP=rvBPXQ&dP`eKSC9@0=O927Llg=A}Cl-5qFf1T3IDIT2doeRPGb|uB
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delta 168
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PY%{yUFP6>!M3|WY8=x;N

diff --git a/pdbbind/.DS_Store b/pdbbind/.DS_Store
index 92970fb4d62a3f08a4b664ce061912687d7205cb..127f8c2b22476e0588d28754832f528d5b91c879 100644
GIT binary patch
delta 108
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delta 88
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Hl=cAtk^ULc

diff --git a/pdbbind/python/utils.py b/pdbbind/python/utils.py
index 6200758..9893863 100644
--- a/pdbbind/python/utils.py
+++ b/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]):
diff --git a/tensorflow/.DS_Store b/tensorflow/.DS_Store
index 716f99a325df2a410f6bde855eb845590c743960..78b518450f7814cf1e64a2746fb257c26be38a71 100644
GIT binary patch
delta 116
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delta 73
zcmZn(XbITxSzvOS<hjWQ1Z5a4H{TWfz{+@H@;UJaLGkKpb7LI^Q)9zg9ffLhbA!nV
b5@L)qCJRc*GtS&RT_THTljvC{uwqjH@)a4e

diff --git a/tensorflow/script/.DS_Store b/tensorflow/script/.DS_Store
index 4769f01e1bf0b407d7af735ce268cfc6ed6645e5..c750a24b793277fca83a4cc93f93e21b4cb8cb62 100644
GIT binary patch
delta 18
ZcmZn(XbISmC&<V!d7_~3<|e@=F#tUm1^)m5

delta 18
ZcmZn(XbISmC&<V+d7_~3<|e@=F#tUw1^@s6

diff --git a/tensorflow/script/test_reg_model.py b/tensorflow/script/test_reg_model.py
index 080f9eb..96b2ea0 100644
--- a/tensorflow/script/test_reg_model.py
+++ b/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()
\ No newline at end of file