Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://rasbt.github.io/biopandas
Working with molecular structures in pandas DataFrames
https://rasbt.github.io/biopandas
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 2 months ago
JSON representation
Working with molecular structures in pandas DataFrames
- Host: GitHub
- URL: https://rasbt.github.io/biopandas
- Owner: BioPandas
- License: bsd-3-clause
- Created: 2015-11-21T00:00:14.000Z (almost 9 years ago)
- Default Branch: main
- Last Pushed: 2024-05-06T14:08:02.000Z (6 months ago)
- Last Synced: 2024-05-22T01:48:25.576Z (6 months ago)
- Topics: bioinformatics, computational-biology, drug-discovery, mol2, molecular-structures, molecule, molecules, pandas-dataframe, pdb, pdb-files, protein-structure
- Language: Python
- Homepage: https://BioPandas.github.io/biopandas/
- Size: 21.9 MB
- Stars: 686
- Watchers: 18
- Forks: 117
- Open Issues: 27
-
Metadata Files:
- Readme: README.md
- Contributing: docs/CONTRIBUTING.md
- License: LICENSE.txt
- Code of conduct: .github/CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-small-molecule-ml - BioPandas
README
**Working with molecular structures in pandas DataFrames**
[](https://travis-ci.org/rasbt/biopandas)
[](https://ci.appveyor.com/project/rasbt/biopandas/branch/master)
[](https://coveralls.io/github/rasbt/biopandas?branch=master)
[](https://pypi.python.org/pypi/biopandas/)
[](https://github.com/rasbt/biopandas/blob/master/LICENSE)
[](http://joss.theoj.org/papers/10.21105/joss.00279)
[](https://github.com/rasbt/biopandas/discussions)
## Links
- Documentation: [https://BioPandas.github.io/biopandas/](https://BioPandas.github.io/biopandas/)
- Source code repository: [https://github.com/rasbt/biopandas](https://github.com/rasbt/biopandas)
- PyPI: [https://pypi.python.org/pypi/biopandas](https://pypi.python.org/pypi/biopandas)
- How to contribute: [https://biopandas.github.io/biopandas/CONTRIBUTING/](https://biopandas.github.io/biopandas/CONTRIBUTING/)
- Changelog: [./docs/sources/CHANGELOG.md](./docs/sources/CHANGELOG.md)
If 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.
As 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.
So, 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!
## Examples
```python
# Initialize a new PandasPdb object
# and fetch the PDB file from rcsb.org
>>> from biopandas.pdb import PandasPdb
>>> ppdb = PandasPdb().fetch_pdb('3eiy')
>>> ppdb.df['ATOM'].head()
```
```python
# Load structures from your drive and compute the
# Root Mean Square Deviation
>>> from biopandas.pdb import PandasPdb
>>> pl1 = PandasPdb().read_pdb('./docking_pose_1.pdb')
>>> pl2 = PandasPdb().read_pdb('./docking_pose_2.pdb')
>>> r = PandasPdb.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
s='hydrogen', invert=True)
>>> print('RMSD: %.4f Angstrom' % r)
RMSD: 2.6444 Angstrom
```
## Quick Install
- install the latest version (from GitHub): `pip install git+git://github.com/rasbt/biopandas.git#egg=biopandas`
- install the latest PyPI version: `pip install biopandas`
- install biopandas via conda-forge: `conda install biopandas -c conda-forge`
#### Requirements
- [Python](https://www.python.org) >=3.7
- [NumPy](http://www.numpy.org) >= 1.11.2
- [SciPy](https://www.scipy.org/scipylib/index.html) >= 0.18.1
- [Pandas](http://pandas.pydata.org) >= 0.19.1
For more information, please see [https://BioPandas.github.io/biopandas/installation/](https://BioPandas.github.io/biopandas/installation/).
### Cite as
If you use BioPandas as part of your workflow in a scientific publication, please consider citing the BioPandas repository with the following DOI:
- 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.
```
@article{raschkas2017biopandas,
doi = {10.21105/joss.00279},
url = {http://dx.doi.org/10.21105/joss.00279},
year = {2017},
month = {jun},
publisher = {The Open Journal},
volume = {2},
number = {14},
author = {Sebastian Raschka},
title = {BioPandas: Working with molecular structures in pandas DataFrames},
journal = {The Journal of Open Source Software}
}
```