Installation instructions

Bept is a cross-platform tool and can be installed on MacOS, Linux and Windows through below-mentioned ways -

Installation

Using pip

You can download bept from PyPI using pip. Run the below command to install -

pip install bept

If you want to use it once without installing, you can use the below command -

pipx bept --help

If you are using uv, you can use-

uvx bept --help

Homebrew

You can download bept from Homebrew by running the below command -

brew install anirudhg07/anirudhg07/bept

Building from source

bept has been made using uv python package manager. You can install uv and run the below commands to install bept -

git clone https://github.com/IISc-Software-iGEM/bept.git
cd bept
pip install .

Check if the tool is successfully installed by running bept --help and you are good to go!

Dependencies

BEPT mainly uses pdb2pqr and apbs tool for running the electrostatics analysis. You need to have these tools installed on your system before running BEPT.

pdb2pqr is shipped with BEPT and you don’t need to install it separately. The latest version on Pypi will be installed automatically.
apbs is not shipped with BEPT and you need to install it separately. You can download it from APBS official website, or as mentioned below.

If you are manually installing the tool, make sure the dependencies are installed which are mentioned in the requirements.txt file by running -

pip install -r requirements.txt

If you downloading via Pypi or Homebrew, these dependencies will be installed automatically.

APBS and PDB2PQR Installation

bept focusses on the automation of the process of running PDB2PQR and APBS. pdb2pqr is installed along with bept so you need not worry. To install APBS, you can follow the below steps -

MacOS

sudo port install apbs

Linux

sudo apt-get install apbs

For Windows, follow the instructions mentioned in the official APBS website here

Once all the dependencies are installed, you should be able to run bept --help and get the help message.