pdb-tools
A dependency-free cross-platform swiss army knife for PDB files.
Science Score: 54.0%
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✓codemeta.json file
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✓DOI references
Found 6 DOI reference(s) in README -
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Low similarity (17.2%) to scientific vocabulary
Keywords
Repository
A dependency-free cross-platform swiss army knife for PDB files.
Basic Info
- Host: GitHub
- Owner: haddocking
- License: apache-2.0
- Language: Python
- Default Branch: master
- Homepage: https://haddocking.github.io/pdb-tools/
- Size: 968 KB
Statistics
- Stars: 426
- Watchers: 13
- Forks: 117
- Open Issues: 26
- Releases: 13
Topics
Metadata Files
README.md
pdb-tools
A swiss army knife for manipulating and editing PDB files.
Looking for the other pdb-tools?
The Harms lab maintains a set of tools also called pdbtools, which perform a
slightly different set of functions. You can find them here.
About
Manipulating PDB files is often painful. Extracting a particular chain or set of residues, renumbering residues, splitting or merging models and chains, or just ensuring the file is conforming to the PDB specifications are examples of tasks that can be done using any decent parsing library or graphical interface. These, however, almost always require 1) scripting knowledge, 2) time, and 3) installing one or more programs.
pdb-tools were designed to be a swiss-knife for the PDB format. They have no
external dependencies, besides obviously the Python programming language.
They are the descendant of a set of old FORTRAN77 programs that had the
particular advantage of working with streams, i.e. the output of one script
could be piped into another. Since FORTRAN77 is a pain too, I rewrote them in
Python and added a few more utilities.
The philosophy of the scripts is simple: one script, one task. If you want to do two things, pipe the scripts together. Requests for new scripts will be taken into consideration - use the Issues button or write them yourself and create a Pull Request.
Installation Instructions
pdb-tools are available on PyPi and can be installed though pip. This is the
recommended way as it makes updating/uninstalling rather simple:
bash
pip install pdb-tools
Because we use semantic versioning in the development of pdb-tools, every bugfix
or new feature results in a new version of the software that is automatically published
on PyPI. As such, there is no difference between the code on github and the latest version
you can install with pip. To update your installation to the latest version of the code
run:
bash
pip install --upgrade pdb-tools
What can I do with them?
The names of the tools should be self-explanatory. Their command-line interface is also pretty consistent. Therefore, here is a couple of examples to get you started:
Downloading a structure
bash pdb_fetch 1brs > 1brs.pdb # 6 chains pdb_fetch -biounit 1brs > 1brs.pdb # 2 chainsRenumbering a structure
bash pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdbSelecting chain(s)
bash pdb_selchain -A 1brs.pdb > 1brs_A.pdb pdb_selchain -A,D 1brs.pdb > 1brs_AD.pdbDeleting hydrogens
bash pdb_delelem -H 1brs.pdb > 1brs_noH.pdbSelecting backbone atoms
bash pdb_selatom -CA,C,N,O 1brs.pdb > 1brs_bb.pdbSelecting chains, removing HETATM, and producing a valid PDB file
bash pdb_selchain -A,D 1brs.pdb | pdb_delhetatm | pdb_tidy > 1brs_AD_noHET.pdb
Note: On Windows the tools will have the .exe extension.
What can't I do with them?
Operations that involve coordinates or numerical calculations are usually not in
the scope of pdb-tools. Use a proper library for that, it will be much faster
and scalable. Also, although we provide mmCIF<->PDB converters, we do not support
large mmCIF files with more than 99999 atoms, or 9999 residues in a single chain.
Our tools will complain if you try using them on such a molecule.
Citation
We finally decided to write up a small publication describing the tools. If you used them in a project that is going to be published, please cite us:
Rodrigues JPGLM, Teixeira JMC, Trellet M and Bonvin AMJJ.
pdb-tools: a swiss army knife for molecular structures.
F1000Research 2018, 7:1961 (https://doi.org/10.12688/f1000research.17456.1)
If you use a reference manager that supports BibTex, use this record:
@Article{ 10.12688/f1000research.17456.1,
AUTHOR = { Rodrigues, JPGLM and Teixeira, JMC and Trellet, M and Bonvin, AMJJ},
TITLE = {pdb-tools: a swiss army knife for molecular structures [version 1; peer review: 2 approved]
},
JOURNAL = {F1000Research},
VOLUME = {7},
YEAR = {2018},
NUMBER = {1961},
DOI = {10.12688/f1000research.17456.1}
}
Requirements
pdb-tools should run on Python 2.7+ and Python 3.x. We test on Python 2.7, 3.6,
and 3.7. There are no dependencies.
Installing from Source
Download the zip archive or clone the repository with git. We recommend the git
approach since it makes updating the tools extremely simple.
```bash
To download
git clone https://github.com/haddocking/pdb-tools cd pdb-tools
To update
git pull origin master
To install
python setup.py install ```
Contributing
If you want to contribute to the development of pdb-tools, provide a bug fix,
or a new tools, read our CONTRIBUTING instructions here.
License
pdb-tools are open-source and licensed under the Apache License, version 2.0.
For details, see the LICENSE file.
Owner
- Name: HADDOCK
- Login: haddocking
- Kind: organization
- Location: Utrecht, The Netherlands
- Website: http://bonvinlab.org
- Repositories: 55
- Profile: https://github.com/haddocking
Computational Structural Biology Group @ Utrecht University
Citation (citation.tex)
@article {Rodrigues483305,
author = {Rodrigues, Jo{\~a}o P.G.L.M. and Teixeira, Jo{\~a}o M.C. and Trellet, Mika{\"e}l and Bonvin, Alexandre M.J.J.},
title = {pdb-tools: a swiss army knife for molecular structures},
elocation-id = {483305},
year = {2018},
doi = {10.1101/483305},
publisher = {Cold Spring Harbor Laboratory},
abstract = {The pdb-tools are a collection of Python scripts for working with molecular structure data in the PDB format. They allow users to edit, convert, and validate PDB files, from the command-line, in a simple but efficient manner. The pdb-tools are implemented in Python, without any external dependencies, and are freely available under the open-source Apache License at https://github.com/haddocking/pdb-tools/ and on PyPI (https://pypi.org/project/pdb-tools/).},
URL = {https://www.biorxiv.org/content/early/2018/12/04/483305},
eprint = {https://www.biorxiv.org/content/early/2018/12/04/483305.full.pdf},
journal = {bioRxiv}
}
GitHub Events
Total
- Issues event: 5
- Watch event: 35
- Delete event: 1
- Issue comment event: 15
- Push event: 21
- Pull request review event: 2
- Fork event: 6
- Create event: 2
Last Year
- Issues event: 5
- Watch event: 35
- Delete event: 1
- Issue comment event: 15
- Push event: 21
- Pull request review event: 2
- Fork event: 6
- Create event: 2
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| João Rodrigues | j****s@g****m | 280 |
| joaomcteixeira | j****a@g****m | 115 |
| JoaoRodrigues | j****s | 30 |
| Mikael Trellet | m****t@g****m | 4 |
| Ryan Vandersmith | r****h@g****m | 2 |
| Joao Rodrigues | a****n@g****m | 1 |
| cunlianggeng | c****g@a****r | 1 |
| Alexandre Bonvin | a****n@g****m | 1 |
| CunliangGeng | C****g | 1 |
| Rodrigo V Honorato | r****o@u****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 56
- Total pull requests: 60
- Average time to close issues: 3 months
- Average time to close pull requests: 27 days
- Total issue authors: 29
- Total pull request authors: 9
- Average comments per issue: 3.16
- Average comments per pull request: 2.78
- Merged pull requests: 44
- Bot issues: 0
- Bot pull requests: 1
Past Year
- Issues: 6
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 6
- Pull request authors: 2
- Average comments per issue: 1.17
- Average comments per pull request: 0.5
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- joaomcteixeira (17)
- amjjbonvin (8)
- rvhonorato (4)
- JoaoRodrigues (2)
- jbibbe4 (1)
- mgiulini (1)
- KasperBuskPedersen (1)
- Danielle-314 (1)
- LilySnow (1)
- sbliven (1)
- Mr-MOPAC (1)
- jyesselm (1)
- hw-protein (1)
- PhilippJunk (1)
- andrewsb8 (1)
Pull Request Authors
- joaomcteixeira (29)
- JoaoRodrigues (24)
- dependabot[bot] (2)
- ahmedselim2017 (2)
- rvhonorato (1)
- andrewsb8 (1)
- ntxxt (1)
- ShintaroMinami (1)
- mgiulini (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 15,970 last-month
- Total docker downloads: 9
-
Total dependent packages: 5
(may contain duplicates) -
Total dependent repositories: 14
(may contain duplicates) - Total versions: 69
- Total maintainers: 2
pypi.org: pdb-tools
A swiss army knife for PDB files.
- Homepage: http://bonvinlab.org/pdb-tools
- Documentation: https://pdb-tools.readthedocs.io/
- License: Apache Software License, version 2
-
Latest release: 2.5.0
published over 3 years ago
Rankings
Maintainers (2)
proxy.golang.org: github.com/haddocking/pdb-tools
- Documentation: https://pkg.go.dev/github.com/haddocking/pdb-tools#section-documentation
- License: apache-2.0
-
Latest release: v2.5.2+incompatible
published 7 months ago
Rankings
Dependencies
- actions/checkout v2 composite
- actions/download-artifact v2 composite
- actions/setup-python v2 composite
- actions/upload-artifact v3 composite
- actions/upload-artifact v2 composite
- actions/checkout v1 composite
- actions/setup-python v1 composite
- actions/checkout v2 composite
- ibiqlik/action-yamllint v3 composite