pdb-tools

Logo

A swiss army knife for editing PDB files.

View the Project on GitHub haddocking/pdb-tools

A swiss army knife for manipulating and editing PDB files.

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:

pip install pdb-tools

If you want to install the latest development version, which might give you new features but also some bugs, see here.

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:

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.

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 army knife for the PDB format. 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.

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.

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, J. P. G. L. M., Teixeira, J. M. C., Trellet, M. & Bonvin, A. M. J. J.
pdb-tools: a swiss army knife for molecular structures. bioRxiv (2018). 
doi:10.1101/483305

If you use a reference manager that supports BibTex, use this record:

@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}
}

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.

# 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.