ProteinPocketDetection

Introduction

This is the source code for paper "Protein Pocket Detection via Convex Hull Surface Evolution and Associated Reeb Graph".
This only supports Linux OS.

Dependencies

Make sure all the following libraries installed in your system.

Boost
Command: sudo apt-get install libboost-all-dev
OpenEXR
Command: sudo apt-get install libopenexr-dev
TBB
Command: sudo apt-get install libtbb-dev
CGAL
Command: sudo apt-get install libcgal-dev libcgal-qt5-dev
OpenVDB
Command: sudo apt-get install libopenvdb-dev

Building

1. Create a new folder under root directory
   
2. Command "cmake .."
   
3. Command "make"
   

Usage

./CavityDetection obj_file xyzr_file minimum_depth minimum_area minimum_volume

./CavityDetection: the executable
obj_file: molecular surface model obj file.
xyzr_file: atoms information file, xyz coordinate and radius per line for each atom.
minimum_depth: minimum required pocket depth
minimum_area: minimum required pocket cross-section area
minimum_volume: minimum required pocket volume.