Installing the software

        

          Software to be installed
            fPocket - Used detect cavities in a molecular structure
            PyMOL - Used to visualize the structure of the molecules
            AutoDoc Vina - This is the software that acutally calculates the docking strength.
            Open Babel - Tools used convert between differnt file formats  

          Protech your PATH, some of the installs may trash your PATH
            export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
          
          Update your computer
            sudo apt updates
            sudo apt upgrade
          
          Prerequisites - need to install the other software
            sudo apt install -y build-essential git cmake libboost-all-dev libnetcdf-dev nvidia-cuda-toolkit
          
          fPocket
            mkdir software
            cd software
            git clone https://github.com/Discngine/fpocket.git
            cd fpocket
            make
            sudo make install
          PyMOL
            cd ..
            wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
            bash Miniconda3-latest-Linux-x86_64.sh
            
            You will be asked some quistions during the install, please answer as shown below:
              Do  you accept the license terms? -> yes
              - Press ENTER to confirm the location - ENTER
              Do you wish to update your shell profile to automatically initialize conda?
              This will activate conda on startup and change the command prompt when activated.
              If you'd prefer that conda's base environment not be activated on startup,
                run the following command when conda is activated:

              conda config --set auto_activate_base false

              Note: You can undo this later by running `conda init --reverse $SHELL`

              Proceed with initialization? yes

            source ~/.bashrc
          
          Open Babel
            cd software/ 
            conda create -n biolab -c conda-forge pymol-open-source openbabel -y
            
            Accept terms:
              conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main
              conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r
          
          Auto-Doc Vina GPU - you will need a github account and token
            cd ~/software
          
            git clone https://github.com/DeltaGroupNJUPT/Vina-GPU-2.1.git
          
            cd Vina-GPU-2.1/AutoDock-Vina-GPU-2.1
          
            set up paths to cuda
              export OPENCL_LIB_PATH=/usr/lib/x86_64-linux-gnu
              export OPENCL_INC_PATH=/usr/include
            
            g++ -o AutoDock-Vina-GPU-2-1 \
            -I./lib -I./OpenCL/inc -I./main \
            -I/usr/include \
            ./main/main.cpp ./lib/*.cpp ./OpenCL/src/wrapcl.cpp \
            -O3 \
            -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lOpenCL -lpthread -lstdc++fs \
            -DOPENCL_2_0 -DNVIDIA_PLATFORM -DSMALL_BOX -DNDEBUG -DBUILD_KERNEL_FROM_SOURCE \
            -DBOOST_TIMER_ENABLE_DEPRECATED

            git clone https://github.com/DeltaGroupNJUPT/Vina-GPU.git

            cd Vina-GPU-2.1/AutoDock-Vina_GPU2.1
            
            rm Makefile

            nano Makefile, use this as your Makefile:
              # 1. Path setup - using relative paths to avoid "shidi" errors
              BOOST_LIB_PATH = /usr/lib/x86_64-linux-gnu
              OPENCL_LIB_PATH = /usr/local/cuda

              # 2. Include paths (The -I flags)
              BOOST_INC_PATH = -I/usr/include
              VINA_GPU_INC_PATH = -I./lib -I./OpenCL/inc
              OPENCL_INC_PATH = -I$(OPENCL_LIB_PATH)/include

              # 3. Library paths and flags (The -L and -l flags)
              LIB_PATH = -L$(BOOST_LIB_PATH) -L$(OPENCL_LIB_PATH)/lib64
              LIB_FLAGS = -lboost_program_options -lboost_thread -lboost_system -lboost_filesystem -lboost_timer -lOpenCL -lstdc++ -lstdc++fs -lm -lpthread

              # 4. Source files
              # Removed the problematic /libs/thread/src/pthread/ paths
              SRC = ./lib/*.cpp ./OpenCL/src/wrapcl.cpp

              # 5. Compiler settings
              GPU_PLATFORM = -DNVIDIA_PLATFORM
              OPENCL_VERSION = -DOPENCL_3_0
              DOCKING_BOX_SIZE = -DSMALL_BOX
              MACRO = $(OPENCL_VERSION) $(GPU_PLATFORM) $(DOCKING_BOX_SIZE) -DBOOST_TIMER_ENABLE_DEPRECATED

              all: out

              out: ./main/main.cpp
                gcc -o AutoDock-Vina-GPU-2-1 $(BOOST_INC_PATH) $(VINA_GPU_INC_PATH) $(OPENCL_INC_PATH) ./main/main.cpp -O3 $(SRC) $(LIB_FLAGS) $(LIB_PATH) $(MACRO) -DNDEBUG

              source: ./main/main.cpp
                gcc -o AutoDock-Vina-GPU-2-1 $(BOOST_INC_PATH) $(VINA_GPU_INC_PATH) $(OPENCL_INC_PATH) ./main/main.cpp -O3 $(SRC) $(LIB_FLAGS) $(LIB_PATH) $(MACRO) -DNDEBUG -DBUILD_KERNEL_FROM_SOURCE

              clean:
                rm -f AutoDock-Vina-GPU-2-1

            Save make file by doing ctrl-o then ctrl-x

            nano OpenCl/src/wrapcl.cpp
            change #include  to #include "wrapcl.h"

            make clean
            make source