Improvised CLI - BEPT

Bept - Beginner friendly Electrostatics for Protein analysis Tool, is built by IISc-Software Team and future juniors iGEMers from Indian Institute of Science, Bengaluru India, for iGEM 2024.

Bept is a beginner-friendly tool for analysis proteins which uses functionalities of pdb2pqr and apbs command line tools, but making them more beginner friendly, making it for you to learn their usages without undergoing the pain of reading the documentation. The tool is meant to target growing scientists interested in protein electrostatics but scared of using Terminal command line tool.

Bept is cross-platform and can be installed on MacOS, Linux and Windows. It is built using Python, managed by uv package manager.

Table of Contents

• Features
• Preview
  • Interactive mode for generating PDB2PQR and APBS input files
  • Generating PQR, Potential DX and BEPT files
  • Automating the process of running PDB2PQR and APBS
• Generating Template Python codes for Pymol
• Installation
  • Using pip
  • Homebrew
  • Docker
  • Building from source
• APBS and PDB2PQR
• Dependencies
• Bept generated the files, now what?
• Too hard to understand even Bept?
• Documentation
• Our Team
• Citations and Acknowledgements

Features

• Interactively generate pdb2pqr command line and APBS .in input files without looking into deep documentation.
• Generate the PQR, Potential DX and BEPT special .bept file containing all the information you need for a protein.
• Automate the process of running PDB2PQR and APBS with optional interactive modes.
• Generate data on surface residues along with calculating SASA values.
• Bept provides PyMol python pre-made template codes for various functionalities.
• Save your .in files in cache for future references.
• Save your PDB2PQR commands in history so you no need to generate it again.
• If you feel understanding how to write the command itself, don't worry, Bept has a friendly UI for that too.
• Read the docs of the tool directly from the CLI in an interactive way.
• Experience bept's extreme user-friendliness, color-coded outputs and error handling and make Electrostatics analysis a breeze!

Preview

Here is series of examples of how to use the tool:

Interactive mode for generating PDB2PQR and APBS input files

Here is how you can generate PQR files with BEPT -

pdb2pqr_gen.mov

Here is how you can edit APBS Input files -

apbs_gen.mov

Generating PQR, Potential DX and BEPT files

gen_dx_cube.mov

Automating the process of running PDB2PQR and APBS

automation_cmd.mov

Generating Template Python codes for Pymol

bept_pymol.mov

Installation

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

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

Docker

You can use the docker image to run bept by pulling the bept image from DockerHub by running the below command -

docker pull anirudhg07/bept

If you do not want to download and run the image directly, you can use the below command -

docker run -it --rm anirudhg07/bept --help

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!

APBS and PDB2PQR

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

• Windows require manual installation. Please check APBS official website for detailed information.

Dependencies

Apart from APBS and PDB2PQR commands, Bept uses python libraries like rich, rich-click, textual, beaupy, etc. for the interactive and colorful setup provided. These dependencies are present in the requirements.txt which are automatically installed when you install via Pypi and Homebrew. You can download these dependencies by the following command -

pip install -r requirements.txt

For windows, you might need to set the PATH variable where the tool is downloaded.

Bept generated the files, now what?

After generating pqr, dx or cube files, you can open them in Pymol to visualise the proteins, their electrostatic gradient maps and much more.

Note

The .bept is our custom made filetype to contain data about the protein, however it is not a globally recognised filetype hence you cannot input it in Pymol. Use these files for your own analysis.

Here is an example of visualisation of 1l2y protein after opening the cube and pqr file generated in Pymol -

Too hard to understand even Bept?

We've got you covered, Bept has a very nice UI for generating the commands for you, powered by trogon. You can just write the file paths and choose the options and the command will be generated for you. You can use it by running bept ui.

bept_ui.mov

Documentation

Bept provides a very nice UI for reading documentation offline in your terminal anytime. You can read it with bept docs. These documentations are also present as it is in docs.

bept_docs.mov

You can also read the docs online at ReadTheDocs.

For any queries or issues, feel free to raise an issue in the repository.

Our Team

The project was made by members of IISc-Software Team along with the upcoming iGEMers among undergraduates from IISc Bengaluru.

• Anirudh Gupta(Maintainer, Project Leader) - Analysis, History management, Integration of features with CLI.
• Aditya Thakkar - APBS interactive generation, Protein Surface Residues output & SASA calculation.
• Kishan Gowda - APBS interactive generation and Textual base PDB2PQR interactive command generation.
• Akshita Sunsugu Palaniswami - Beaupy based PDB2PQR interactive command generation.
• G Hasini - Software Testing
• Deeptam Bhar - Interactive documentation and Bept LOGO design.
• Aditey Nandan - Biological Backend and Documentation
• Ritabrata Saha - Biological Backend and Documentation
• Shreyan Priyadarshi - Biological Backend and Documentation
• Soham Paul - Biological Backend and Documentation

Read our blog about bept here. Also read our iGEM wiki page for BEPT here.

Citations and Acknowledgements

PDB2PQR -

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei G-W, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci, 27 (1), 112-128, 2018. https://doi.org/10.1002/pro.3280

APBS -

Jurrus E, Engel D, Star K, Monson K, Brandi J, Felberg LE, Brookes DH, Wilson L, Chen J, Liles K, Chun M, Li P, Gohara DW, Dolinsky T, Konecny R, Koes DR, Nielsen JE, Head-Gordon T, Geng W, Krasny R, Wei G-W, Holst MJ, McCammon JA, Baker NA. Improvements to the APBS biomolecular solvation software suite. Protein Sci, 27 (1), 112-128, 2018. https://doi.org/10.1002/pro.3280

Note

The dx2cube functionality for analysis have been adapted from pdb2pqr Github repository and has been well acknowledged in the source code.

License

BEPT is under MIT License and you can use it for free. If you like the tool, please share with others.

If you have any issues or want to contribute, please raise an issue in the repository.