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A swiss army knife for PDB files.

Project description

pdb-tools

PyPI version Travis (.org) branch AppVeyor branch codecov

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:

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 usage is also pretty consistent. Therefore, here is a couple of examples to get you started:

  • Downloading a structure

    pdb_fetch 1ctf > 1ctf.pdb
    pdb_fetch -biounit 1brs > 1brs_biounit.pdb
    
  • Renumbering a structure

    pdb_reres -1 1ctf.pdb > 1ctf_renumbered.pdb
    
  • Extracting a particular chain

    pdb_selchain -A 1brs_biounit.pdb > 1brs_A.pdb
    
  • Downloading, extracting a chain, and extracting its aa sequence

    pdb_fetch 1brs | pdb_selchain -A | pdb_toseq > 1brs_A.fasta
    

What can't I do with them?

mmCIF files are not supported. There might be a sister repository mmcif-tools one day. Also, 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.

Citation

There is no publication (yet!) for pdb-tools, but if you use them and want to cite them use this DOI item.

DOI

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/JoaoRodrigues/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.

Project details


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