From 69d53c4f0878ff7e6ed74f2ed211e9e0c6b8dd84 Mon Sep 17 00:00:00 2001 From: Qinqing Liu Date: Tue, 17 Nov 2020 14:20:40 -0500 Subject: [PATCH] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index eb0b9a0..8adb29d 100644 --- a/README.md +++ b/README.md @@ -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 @@ -15,7 +15,7 @@ bash data_download.sh 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 @@ -63,7 +63,7 @@ cd python 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.