BioPandas

BioPandas: Working with molecular structures in pandas DataFrames - Published in JOSS (2017)

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 10 DOI reference(s) in README
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Academic publication links
Links to: joss.theoj.org
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Committers with academic emails
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.5%) to scientific vocabulary

Keywords

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Last synced: 6 months ago · JSON representation

Repository

Working with molecular structures in pandas DataFrames

Basic Info

Host: GitHub
Owner: BioPandas
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://BioPandas.github.io/biopandas/
Size: 22.3 MB

Statistics

Stars: 737
Watchers: 15
Forks: 118
Open Issues: 25
Releases: 18

Topics

bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure

Created over 10 years ago · Last pushed over 1 year ago

Metadata Files

Readme Contributing License Code of conduct

README.md

Logo

Working with molecular structures in pandas DataFrames

Links

Documentation: https://BioPandas.github.io/biopandas/
Source code repository: https://github.com/rasbt/biopandas
PyPI: https://pypi.python.org/pypi/biopandas
How to contribute: https://biopandas.github.io/biopandas/CONTRIBUTING/
Changelog: ./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 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

3eiy 3eiy

```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() ```

3eiy head

```python

Load structures from your drive and compute the

Root Mean Square Deviation

from biopandas.pdb import PandasPdb pl1 = PandasPdb().readpdb('./dockingpose1.pdb') pl2 = PandasPdb().readpdb('./dockingpose2.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 >=3.7
NumPy >= 1.11.2
SciPy >= 0.18.1
Pandas >= 0.19.1

For more information, please see 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} }

Owner

Name: BioPandas
Login: BioPandas
Kind: organization

Repositories: 1
Profile: https://github.com/BioPandas

Working with molecular structures in pandas DataFrames

GitHub Events

Total

Issues event: 1
Watch event: 32
Issue comment event: 3
Pull request review event: 1

Last Year

Issues event: 1
Watch event: 32
Issue comment event: 3
Pull request review event: 1

Committers

Last synced: 7 months ago

All Time

Total Commits: 288
Total Committers: 17
Avg Commits per committer: 16.941
Development Distribution Score (DDS): 0.465

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
rasbt	m**l@s**m	154
Arian Jamasb	a**b@g**m	93
Anton Bushuiev	a**v@g**m	14
Unknown	d**w@p**e	6
AbdulHamid Merii	a**i@o**m	5
huginn	h**n@p**n	4
zehraacarsarica	z**9@g**m	2
Arian Jamasb	a**b@r**m	1
Erik Cederstrand	e**k@c**k	1
Giacomo Nunziati	7****i	1
Grigorev Rostislav	4****n	1
Kieran Didi	5****i	1
Kristian Rother	k**r@a**u	1
Marcin Wojdyr	w**r@g**m	1
Ruibin Liu	r**8@g**m	1
braniii	d**l@p**m	1
tugceoruc	t**4@g**m	1

Committer Domains (Top 20 + Academic)

academis.eu: 1 cederstrand.dk: 1 roche.com: 1 pop-os.localdomain: 1 posteo.de: 1 sebastianraschka.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 45
Total pull requests: 80
Average time to close issues: 9 months
Average time to close pull requests: 8 days
Total issue authors: 28
Total pull request authors: 17
Average comments per issue: 2.13
Average comments per pull request: 1.83
Merged pull requests: 71
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 1
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

rasbt (7)
a-r-j (7)
dominiquesydow (3)
gate-tec (2)
gezmi (2)
mrauha (2)
btyukodi (1)
chendaniely (1)
jaydeepsb (1)
luc-j-bourhis (1)
RMeli (1)
Irlirion (1)
chrischen1 (1)
djberenberg (1)
moorepants (1)

Pull Request Authors

rasbt (40)
a-r-j (20)
kierandidi (4)
gezmi (2)
goniochromatic (2)
dominiquesydow (2)
Irlirion (2)
braniii (1)
SowmyaLR (1)
ecederstrand (1)
tugceoruc (1)
wojdyr (1)
AH-Merii (1)
nunziati (1)
anton-bushuiev (1)

Top Labels

Issue Labels

enhancement (12) bug (4) help wanted (2)

Pull Request Labels

Packages

Total packages: 3
Total downloads: unknown

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 17
(may contain duplicates)
Total versions: 47

proxy.golang.org: github.com/BioPandas/biopandas

Documentation: https://pkg.go.dev/github.com/BioPandas/biopandas#section-documentation
License: bsd-3-clause
Latest release: v0.5.1
published over 1 year ago

Versions: 18
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Stargazers count: 2.4%

Forks count: 2.4%

Average: 6.3%

Dependent packages count: 9.6%

Dependent repos count: 10.8%

Last synced: 6 months ago

proxy.golang.org: github.com/biopandas/biopandas

Documentation: https://pkg.go.dev/github.com/biopandas/biopandas#section-documentation
License: bsd-3-clause
Latest release: v0.5.1
published over 1 year ago

Versions: 18
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Stargazers count: 2.4%

Forks count: 2.5%

Average: 6.3%

Dependent packages count: 9.6%

Dependent repos count: 10.8%

Last synced: 6 months ago

conda-forge.org: biopandas

BioPandas is a library for working with Protein Databank Files(PDB) written in Python 2.7 and Python 3.6.

Homepage: http://github.com/BioPandas/biopandas
License: BSD-3-Clause
Latest release: 0.4.1
published almost 4 years ago

Versions: 11
Dependent Packages: 3
Dependent Repositories: 17

Rankings

Dependent repos count: 8.6%

Average: 14.4%

Dependent packages count: 15.6%

Stargazers count: 15.9%

Forks count: 17.4%

Last synced: 6 months ago

Dependencies

requirements.txt pypi

numpy >=1.16.2
pandas >=0.24.2