Installation
Warning
Currently, the python bindings and the binary installation are two separate processes. The installation of the python bindings does not include the Vina executable, and vice versa.
Unix- and Linux-based OS
Vina is expected to work on x86 and compatible 64-bit Linux systems. The executable for the latest release are available here: https://github.com/ccsb-scripps/AutoDock-Vina/releases.
Running:
./vina_1.2.0_linux_x86_64 --help
If the executable is in your PATH, you can just type “vina –help” instead.
macOS
Vina is expected to work on macOS 10.15 (Catalina) and newer. The executable for the latest release are available here: https://github.com/ccsb-scripps/AutoDock-Vina/releases.
Running:
./vina_1.2.0_macos_x86_64 --help
If the executable is in your PATH, you can just type “vina –help” instead.
Python bindings
AutoDock Vina installation using pip:
Note
When using pip
, it’s good pratice to use a virtual environment and also the easiest solution (see meeko
in Software requirements). An example with the Conda package manager is available further down.
$ pip install -U numpy vina
AutoDock Vina installation in a Conda environment:
The Anaconda Python distribution, which can be download from https://docs.continuum.io/anaconda/install. This is a Python distribution specially designed for scientific applications, with many of the most popular scientific packages preinstalled. Alternatively, you can use Miniconda, which includes only Python itself, plus the Conda package manager.
Begin by installing the most recent 64 bit, Python 3.x version of either Anaconda or Miniconda
Create a dedicated environment for
AutoDock Vina
. This environment can be re-used for installingmeeko
(see Software requirements):
$ conda create -n vina python=3
$ conda activate vina
$ conda config --env --add channels conda-forge
And type the following command to install
NumPy
andAutoDock Vina
:
$ conda install numpy
$ pip install vina
Building from Source
Warning
Building Vina from source is NOT meant to be done by regular users!
- Step 1: Install a C++ compiler suite
Ubuntu/Debian:
sudo apt-get install build-essentials
macOS: Install Xcode from the AppStore and the Command Line Tools (CLT) from the terminal
xcode-select --install
- Step 2: Install Boost and SWIG
Ubuntu/Debian:
sudo apt-get install libboost-all-dev swig
macOS (with Homebrew):
brew install boost swig
Step 3: Build Vina
Start by downloading the lastest version of
AutoDock Vina
from github:$ git clone https://github.com/ccsb-scripps/AutoDock-Vina
To compile the binary (you might need to customize the Makefile by setting the paths to the Boost library):
$ cd AutoDock-Vina/build/linux/release $ make
To compile the Python bindings:
Note
The
Conda
package manager is used here to easily install the several dependencies needed to build theAutodock-Vina
python bindings (see above how to create a dedicated environment).$ conda activate vina $ cd AutoDock-Vina/build/python $ conda install -c conda-forge numpy boost-cpp swig $ rm -rf build dist *.egg-info (to clean previous installation) $ python setup.py build install