{"id":13907210,"url":"https://github.com/BioPandas/biopandas","last_synced_at":"2025-07-18T05:30:55.506Z","repository":{"id":37768407,"uuid":"46593500","full_name":"BioPandas/biopandas","owner":"BioPandas","description":"Working with molecular structures in pandas 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with molecular structures in pandas DataFrames**\n\n\n[![Continuous Integration](https://travis-ci.org/rasbt/biopandas.svg?branch=master)](https://travis-ci.org/rasbt/biopandas)\n[![Build status](https://ci.appveyor.com/api/projects/status/jcp91fvbgmqws30p/branch/master?svg=true)](https://ci.appveyor.com/project/rasbt/biopandas/branch/master)\n[![Code Coverage](https://coveralls.io/repos/rasbt/biopandas/badge.svg?branch=master\u0026service=github)](https://coveralls.io/github/rasbt/biopandas?branch=master)\n[![PyPI Version](https://img.shields.io/pypi/v/biopandas.svg)](https://pypi.python.org/pypi/biopandas/)\n[![License](https://img.shields.io/badge/license-new%20BSD-blue.svg)](https://github.com/rasbt/biopandas/blob/master/LICENSE)\n![Python 3](https://img.shields.io/badge/python-3-blue.svg)\n[![JOSS](http://joss.theoj.org/papers/10.21105/joss.00279/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00279)\n[![Discuss](https://img.shields.io/badge/discuss-github-blue.svg)](https://github.com/rasbt/biopandas/discussions)\n\n\u003chr\u003e\n\n## Links\n- Documentation: [https://BioPandas.github.io/biopandas/](https://BioPandas.github.io/biopandas/)\n- Source code repository: [https://github.com/rasbt/biopandas](https://github.com/rasbt/biopandas)\n- PyPI: [https://pypi.python.org/pypi/biopandas](https://pypi.python.org/pypi/biopandas)\n- How to contribute: [https://biopandas.github.io/biopandas/CONTRIBUTING/](https://biopandas.github.io/biopandas/CONTRIBUTING/)\n- Changelog: [./docs/sources/CHANGELOG.md](./docs/sources/CHANGELOG.md)\n\n\u003cbr\u003e\n\nIf you are a computational biologist, chances are that you cursed one too many times about protein structure files. Yes, I am talking about ye Goode Olde Protein Data Bank format, aka \"PDB files.\" Nothing against PDB, it's a neatly structured format (if deployed correctly); yet, it is a bit cumbersome to work with PDB files in \"modern\" programming languages -- I am pretty sure we all agree on this.\n\nAs machine learning and \"data science\" person, I fell in love with [pandas](http://pandas.pydata.org) DataFrames for handling just about everything that can be loaded into memory.  \nSo, why don't we take pandas to the structural biology world? Working with molecular structures of biological macromolecules (from PDB and MOL2 files) in pandas DataFrames is what BioPandas is all about!\n\n\u003cbr\u003e\n\n## Examples\n\n![3eiy](./docs/img/index/3eiy.png#gh-light-mode-only)![3eiy](./docs/img/index/3eiy_dark.png#gh-dark-mode-only)\n\n```python\n# Initialize a new PandasPdb object\n# and fetch the PDB file from rcsb.org\n\u003e\u003e\u003e from biopandas.pdb import PandasPdb\n\u003e\u003e\u003e ppdb = PandasPdb().fetch_pdb('3eiy')\n\u003e\u003e\u003e ppdb.df['ATOM'].head()\n```\n\n![3eiy head](./docs/img/index/3eiy_head.png#gh-light-mode-only)![3eiy head](./docs/img/index/3eiy_head_dark.png#gh-dark-mode-only)\n\n\u003cbr\u003e\u003cbr\u003e\n\u003cbr\u003e\u003cbr\u003e\n\n\n![3eiy head](./docs/img/index/ligand_rmsd.png#gh-light-mode-only)![3eiy head](./docs/img/index/ligand_rmsd_dark.png#gh-dark-mode-only)\n\n```python\n# Load structures from your drive and compute the\n# Root Mean Square Deviation\n\u003e\u003e\u003e from biopandas.pdb import PandasPdb\n\u003e\u003e\u003e pl1 = PandasPdb().read_pdb('./docking_pose_1.pdb')\n\u003e\u003e\u003e pl2 = PandasPdb().read_pdb('./docking_pose_2.pdb')\n\u003e\u003e\u003e r = PandasPdb.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],\n                       s='hydrogen', invert=True)\n\u003e\u003e\u003e print('RMSD: %.4f Angstrom' % r)\n\nRMSD: 2.6444 Angstrom\n```\n\n\u003cbr\u003e\u003cbr\u003e\n\u003cbr\u003e\u003cbr\u003e\n\n\n## Quick Install\n\n- install the latest version (from GitHub): `pip install git+git://github.com/rasbt/biopandas.git#egg=biopandas`\n- install the latest PyPI version: `pip install biopandas`\n- install biopandas via conda-forge: `conda install biopandas -c conda-forge`\n\n#### Requirements\n\n- [Python](https://www.python.org) \u003e=3.7\n- [NumPy](http://www.numpy.org) \u003e= 1.11.2\n- [SciPy](https://www.scipy.org/scipylib/index.html) \u003e= 0.18.1\n- [Pandas](http://pandas.pydata.org) \u003e= 0.19.1\n\n\nFor more information, please see [https://BioPandas.github.io/biopandas/installation/](https://BioPandas.github.io/biopandas/installation/).\n\n\u003cbr\u003e\u003cbr\u003e\n\u003cbr\u003e\u003cbr\u003e\n\n\n### Cite as\n\nIf you use BioPandas as part of your workflow in a scientific publication, please consider citing the BioPandas repository with the following DOI:\n\n- Sebastian Raschka. Biopandas: Working with molecular structures in pandas dataframes. *The Journal of Open Source Software*, 2(14), jun 2017. doi: 10.21105/joss.00279. URL http://dx.doi.org/10.21105/joss.00279.\n\n```\n@article{raschkas2017biopandas,\n  doi = {10.21105/joss.00279},\n  url = {http://dx.doi.org/10.21105/joss.00279},\n  year  = {2017},\n  month = {jun},\n  publisher = {The Open Journal},\n  volume = {2},\n  number = {14},\n  author = {Sebastian Raschka},\n  title = {BioPandas: Working with molecular structures in pandas DataFrames},\n  journal = {The Journal of Open Source Software}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBioPandas%2Fbiopandas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FBioPandas%2Fbiopandas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FBioPandas%2Fbiopandas/lists"}