update readme

README.md

@@ -1,2 +1,72 @@
 # OctSurf
-
+
+<!-- ## Introduction <a name="introduction"></a> -->
+
+This is the code repository for OctSurf: Efficient Hierarchical Voxel-based Molecular Surface Representation for the Protein-Ligand Affinity Prediction.
+
+### Experiments
+
+#### PDBbind download  
+```angular2
+cd pdbbind
+bash data_download.sh
+```
+
+#### Set-up enviroment
+```angular2
+# compile java
+cd pdbbind/java
+javac -cp cdk-2.3-SNAPSHOT.jar Surface_for_single.java
+
+# compile cpp
+cd ../../
+cd octree/external && git clone --recursive https://github.com/wang-ps/octree-ext.git
+cd .. && mkdir build && cd build
+cmake ..  && cmake --build . --config Release
+export PATH=`pwd`:$PATH
+
+# set-up TF enviroment
+conda create -n OctSurf_env tensorflow-gpu==1.14.0
+conda activate OctSurf_env
+conda install -c conda-forge yacs tqdm
+pip install -U openbabel
+
+cmake .. -DUSE_CUDA=ON && make
+
+cd ../../tensorflow/libs
+python build.py
+```
+
+#### Octree Generation Example
+```angular2
+cd pdbbind/data_folder/refined-set/1a1e
+bash ../octree_for_single.sh
+
+# visualization
+pip install vtk
+cd ../../../../visualize octree_parse.py
+```
+#### CNN modeling
+
+- prepare the data 
+```angular2
+bash data_prepare_model.sh
+```
+- train model 
+```angular2
+cd tensorflow/script
+python run_cls.py --config configs/vgg_depth6.yaml
+```
+
+- test performance 
+```angular2
+python test_reg_ave.py --config configs/vgg_depth6_test.yaml
+```
+
+### Acknowledgments
+Code is inspired by [O-CNN](https://wang-ps.github.io/O-CNN.html).
+
+The code is released under the **MIT license**.  
+Please contact us (Qinqing Liu qinqing.liu@uconn.edu, Minghu Song minghu.song@uconn.edu )
+if you have any problems about our implementation.  
+

pdbbind/bash_scripts/data_prepare_points.sh

@@ -0,0 +1,13 @@
+for D in ./*/;
+do
+    echo "${D}";
+    cd "${D}";
+    java -cp /home/qil15006/2020Summer/OCNN_Jun26_2020/pdbbind/java/cdk-2.3-SNAPSHOT.jar:/home/qil15006/2020Summer/OCNN_Jun26_2020/pdbbind/java Surface_for_single 6 ico pdbbind;
+    /home/qil15006/.conda/envs/tf-OCNN/bin/python /home/qil15006/2020Summer/OCNN_Jun26_2020/pdbbind/write_complex.py
+    /home/qil15006/.conda/envs/tf-OCNN/bin/python /home/qil15006/2020Summer/OCNN_Jun26_2020/pdbbind/atomic_feature.py
+    /home/qil15006/2020Summer/OCNN_Jun26_2020/octree/build/pdb_to_points --complex_id file_list.txt
+    # uncomment if need octree
+    #mkdir octree_folder
+    #/home/qil15006/2020Summer/OCNN_Jun26_2020/octree/build/qq_octree_rotate --depth 5 --filenames point_list.txt --output_path ./octree_folder
+    cd ..;
+done