| Name | bept JSON |
| Version |
0.1.0
JSON |
| download |
| home_page | None |
| Summary | BEPT is a Beginner friendly Electrostatics for Protein analysis Tool, a cross-platform interactive and user-friendly tool for protein electrostatics using APBS and PDB2PQR. |
| upload_time | 2024-10-02 06:27:29 |
| maintainer | Anirudh Gupta |
| docs_url | None |
| author | Anirudh Gupta, Akshita Sunsugu Panliswami, Aditya Thakkar, Kishan Gowda, G Hasini, Soham Paul, Aditey Nandan, Ritabrata Saha, Shreyan Priyadarshi, Deeptam Bhar |
| requires_python | >=3.11 |
| license | MIT License Copyright (c) 2024 IISc Software iGEM Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
apbs
bept
cli
cube
dx2cube
electrostatics
pdb2pqr
protein
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Improvised CLI - BEPT 
<p align="center">
<a><img width=700 alt = "bept logo" src="https://github.com/user-attachments/assets/d9bc6905-1082-42a3-a36d-04e0b253b27c" </a>
</a>
</p>
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.
## 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 -
https://github.com/user-attachments/assets/64ee9e6f-20e1-4898-878c-c6203a4c4b38
Here is how you can edit APBS Input files -
https://github.com/user-attachments/assets/3b82c678-ae24-4d9f-a797-1c2a062230db
### Generating PQR, Potential DX and BEPT files
https://github.com/user-attachments/assets/df7178af-494c-43dd-bb27-14e45764e523
### Automating the process of running PDB2PQR and APBS
https://github.com/user-attachments/assets/93476c8b-df43-45d0-a7fe-79aa359f2f09
## Generating Template Python codes for Pymol
https://github.com/user-attachments/assets/49268543-65f3-49b4-92dc-d724886e9df5
## 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 -
```bash
pip install bept
```
If you want to use it once without installing, you can use the below command -
```bash
pipx bept --help
```
If you are using `uv`, you can use-
```bash
uvx bept --help
```
### Homebrew
You can download bept from Homebrew by running the below command -
```bash
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` -
```bash
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
```bash
sudo port install apbs
```
- Linux
```bash
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](https://github.com/Textualize/rich), [rich-click](https://github.com/ewels/rich-click), [textual](https://github.com/Textualize/textual), [beaupy](https://github.com/petereon/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 -
```bash
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](https://github.com/textualize/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`.
https://github.com/user-attachments/assets/6058a9fc-2642-4ef0-80f1-2972f0c9218b
## 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](/docs).
https://github.com/user-attachments/assets/86d8e34a-f898-46f0-891c-f3c47b5acfcb
You can also read the docs online at [ReadTheDocs](https://bept.readthedocs.io/en/latest/).
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
- Kishan Gowda - APBS interactive generation
- Akshita Sunsugu Palaniswami - PDB2PQR interactive generation
- G Hasini - Software Testing
- Deeptam Bhar - Interactive documentation
- Aditey Nandan - Biological Backend and Documentation
- Ritabrata Saha - Biological Backend and Documentation
- Shreyan Priyadarshi - Biological Backend and Documentation
- Soham Paul - Biological Backend and Documentation
## Citations and Acknowledgements
PDB2PQR -
```bibtex
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 -
```bibtex
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](https://github.com/Electrostatics/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.
Raw data
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"description": "# Improvised CLI - BEPT \n\n<p align=\"center\">\n <a><img width=700 alt = \"bept logo\" src=\"https://github.com/user-attachments/assets/d9bc6905-1082-42a3-a36d-04e0b253b27c\" </a>\n</a>\n</p>\n\nBept - 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.\n\nBept 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.\n\nBept is cross-platform and can be installed on MacOS, Linux and Windows. It is built using Python, managed by `uv` package manager.\n\n## Features\n\n- Interactively generate pdb2pqr command line and APBS `.in` input files without looking into deep documentation.\n- Generate the PQR, Potential DX and BEPT special `.bept` file containing all the information you need for a protein.\n- Automate the process of running PDB2PQR and APBS with optional interactive modes.\n- Generate data on surface residues along with calculating SASA values.\n- Bept provides PyMol python pre-made template codes for various functionalities.\n- Save your `.in` files in cache for future references.\n- Save your PDB2PQR commands in history so you no need to generate it again.\n- If you feel understanding how to write the command itself, don't worry, Bept has a friendly UI for that too.\n- Read the docs of the tool directly from the CLI in an interactive way.\n- Experience bept's extreme user-friendliness, color-coded outputs and error handling and make Electrostatics analysis a breeze!\n\n## Preview\n\nHere is series of examples of how to use the tool:\n\n### Interactive mode for generating PDB2PQR and APBS input files\n\nHere is how you can generate PQR files with BEPT -\n\nhttps://github.com/user-attachments/assets/64ee9e6f-20e1-4898-878c-c6203a4c4b38\n\nHere is how you can edit APBS Input files -\n\nhttps://github.com/user-attachments/assets/3b82c678-ae24-4d9f-a797-1c2a062230db\n\n### Generating PQR, Potential DX and BEPT files\n\nhttps://github.com/user-attachments/assets/df7178af-494c-43dd-bb27-14e45764e523\n\n### Automating the process of running PDB2PQR and APBS\n\nhttps://github.com/user-attachments/assets/93476c8b-df43-45d0-a7fe-79aa359f2f09\n\n## Generating Template Python codes for Pymol\n\nhttps://github.com/user-attachments/assets/49268543-65f3-49b4-92dc-d724886e9df5\n\n## Installation\n\nBept is a cross-platform tool and can be installed on MacOS, Linux and Windows through below-mentioned ways -\n\n### Using pip\n\nYou can download bept from PyPI using pip. Run the below command to install -\n\n```bash\npip install bept\n```\n\nIf you want to use it once without installing, you can use the below command -\n\n```bash\npipx bept --help\n```\n\nIf you are using `uv`, you can use-\n\n```bash\nuvx bept --help\n```\n\n### Homebrew\n\nYou can download bept from Homebrew by running the below command -\n\n```bash\nbrew install anirudhg07/anirudhg07/bept\n```\n\n### Building from source\n\n`bept` has been made using `uv` python package manager. You can install `uv` and run the below commands to install `bept` -\n\n```bash\ngit clone https://github.com/IISc-Software-iGEM/bept.git\ncd bept\npip install .\n```\n\nCheck if the tool is successfully installed by running `bept --help` and you are good to go!\n\n## APBS and PDB2PQR\n\n`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 -\n\n- MacOS\n\n```bash\nsudo port install apbs\n```\n\n- Linux\n\n```bash\nsudo apt-get install apbs\n```\n\n- Windows require manual installation. Please check APBS official website for detailed information.\n\n## Dependencies\n\nApart from APBS and PDB2PQR commands, Bept uses python libraries like [rich](https://github.com/Textualize/rich), [rich-click](https://github.com/ewels/rich-click), [textual](https://github.com/Textualize/textual), [beaupy](https://github.com/petereon/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 -\n\n```bash\npip install -r requirements.txt\n```\n\nFor windows, you might need to set the PATH variable where the tool is downloaded.\n\n## Bept generated the files, now what?\n\nAfter generating `pqr`, `dx` or `cube` files, you can open them in Pymol to visualise the proteins, their electrostatic gradient maps and much more.\n\n> [!Note]\n> 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.\n\nHere is an example of visualisation of `1l2y` protein after opening the `cube` and `pqr` file generated in Pymol -\n\n\n\n## Too hard to understand even Bept?\n\nWe've got you covered, Bept has a very nice UI for generating the commands for you, powered by [trogon](https://github.com/textualize/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`.\n\nhttps://github.com/user-attachments/assets/6058a9fc-2642-4ef0-80f1-2972f0c9218b\n\n## Documentation\n\nBept 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](/docs).\n\nhttps://github.com/user-attachments/assets/86d8e34a-f898-46f0-891c-f3c47b5acfcb\n\nYou can also read the docs online at [ReadTheDocs](https://bept.readthedocs.io/en/latest/).\n\nFor any queries or issues, feel free to raise an issue in the repository.\n\n## Our Team\n\nThe project was made by members of IISc-Software Team along with the upcoming iGEMers among undergraduates from IISc Bengaluru.\n\n- Anirudh Gupta(Maintainer, Project Leader) - Analysis, History management, Integration of features with CLI.\n- Aditya Thakkar - APBS interactive generation\n- Kishan Gowda - APBS interactive generation\n- Akshita Sunsugu Palaniswami - PDB2PQR interactive generation\n- G Hasini - Software Testing\n- Deeptam Bhar - Interactive documentation\n- Aditey Nandan - Biological Backend and Documentation\n- Ritabrata Saha - Biological Backend and Documentation\n- Shreyan Priyadarshi - Biological Backend and Documentation\n- Soham Paul - Biological Backend and Documentation\n\n## Citations and Acknowledgements\n\nPDB2PQR -\n\n```bibtex\nJurrus 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. 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